From somesh.kb at gmail.com  Sat Dec  1 06:21:53 2007
From: somesh.kb at gmail.com (Somesh Kumar Bhattacharya)
Date: Sat, 1 Dec 2007 10:51:53 +0530
Subject: [Pw_forum] Pw_forum Digest, Vol 5, Issue 58
In-Reply-To: <be564dcb0711301030t501ee032x8ca224b416a49379@mail.gmail.com>
References: <mailman.1.1196406612.587.pw_forum@pwscf.org>
	<be564dcb0711301029m319c9b06jb568ed33f52914b4@mail.gmail.com>
	<be564dcb0711301030t501ee032x8ca224b416a49379@mail.gmail.com>
Message-ID: <e0e40e0d0711302121v50d74d06h6d4580fa845403ea@mail.gmail.com>

hello Eduardo Menendez,

Thanks a lot for the PP ....................
I will try with this and will report soon incase of any problems
.......................
ciao

Somesh

On Dec 1, 2007 12:00 AM, Eduardo Ariel Menendez Proupin <eariel99 at gmail.com>
wrote:

> Hi,
> Find attached one pseudo for Te. It is not Vanderbilt, but norm conserving
> RRKJ. I had made it ultrasoft before, but there is little difference, as
> long as the 4d electrons are in the core. Exchange correlation is PBE.
> I use it for molecular dynamics setting ecutrho=30,ecutwfc=180, and
> tqr=-true.
>
> Eduardo Menendez
>
>
> 2007/11/30, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>:
> >
> > Send Pw_forum mailing list submissions to
> >         pw_forum at pwscf.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >          http://www.democritos.it/mailman/listinfo/pw_forum
> > or, via email, send a message with subject or body 'help' to
> >          pw_forum-request at pwscf.org
> >
> > You can reach the person managing the list at
> >         pw_forum-owner at pwscf.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Pw_forum digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Te pseudopotentials (Somesh Kumar Bhattacharya)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 30 Nov 2007 11:03:03 +0530
> > From: "Somesh Kumar Bhattacharya" <somesh.kb at gmail.com>
> > Subject: [Pw_forum] Te pseudopotentials
> > To: pw_forum at pwscf.org
> > Message-ID:
> >         <e0e40e0d0711292133s6b27af60k245fd5a9c9210ea8 at mail.gmail.com >
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Dear Users,
> >
> > I wish to do some calculations on CdTe clusters using PWSCF. For this I
> > need
> > Vanderbilt USPP  with PBE exchange correlation.
> > For Cd it exist and I can get from the net. But for Te its not there.
> > Can
> > anyone please provide me with the required PP????
> >
> >
> > Regards,
> >
> > Somesh
> >
> > SOMESH KR. BHATTACHARYA                   Ph.no.- (O)+91-
> > 020-25692678-426
> > JUNIOR RESEARCH FELLOW
> > (M)+919921680580
> > DEPT. OF PHYSICS
> > UNIV. OF PUNE
> > GANESHKHIND
> > PUNE-411007
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> > http://www.democritos.it/pipermail/pw_forum/attachments/20071130/4ea06810/attachment.html
> >
> > ------------------------------
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
> >
> > End of Pw_forum Digest, Vol 5, Issue 58
> > ***************************************
> >
>
>
>
> --
> Eduardo Menendez
>
>
> --
> Eduardo Menendez




-- 
Somesh Kr. Bhattacharya
Department of Physics,
University of Pune,
Ganeshkhind,
Pune - 411007
INDIA
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From serenechan at charteredsemi.com  Sat Dec  1 09:03:01 2007
From: serenechan at charteredsemi.com (serenechan at charteredsemi.com)
Date: Sat, 1 Dec 2007 16:03:01 +0800
Subject: [Pw_forum] CHAN Serene is out of the office.
Message-ID: <OF3D70134E.337029BA-ON482573A4.002C38F9-482573A4.002C38F9@charteredsemi.com>





I will be out of the office starting  12/01/2007 and will not return until
12/06/2007.

Please approach my colleague Ellen Puspitasari, Chong Huey Ming or Tan Soon
Yoeng for all tapeout related matters.


From akohlmey at cmm.chem.upenn.edu  Sat Dec  1 19:37:43 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sat, 1 Dec 2007 13:37:43 -0500
Subject: [Pw_forum] Pw_forum Digest, Vol 5, Issue 58
In-Reply-To: <e0e40e0d0711302121v50d74d06h6d4580fa845403ea@mail.gmail.com>
References: <mailman.1.1196406612.587.pw_forum@pwscf.org>
	<be564dcb0711301029m319c9b06jb568ed33f52914b4@mail.gmail.com>
	<be564dcb0711301030t501ee032x8ca224b416a49379@mail.gmail.com>
	<e0e40e0d0711302121v50d74d06h6d4580fa845403ea@mail.gmail.com>
Message-ID: <7b6913e90712011037t7ffbe00jbcc7c2e6873aad55@mail.gmail.com>

hi!

just a quick remark before you are wondering about the results.

a) it looks like it should be ecutwfc=30
b) for norm-conserving pseudopotentials there is no reason to
    use a density cutoff higher than 4x the wavefunction cutoff.
  => thus ecutrho=120 should sufficient. if not, you'll have to increast both
    ecutwfc and ecutrho.

...and of course the "hardest" pseudopotential and whether you do have
an USPP for another element determines the ultimate choice.

best regards,
     axel.

On Dec 1, 2007 12:21 AM, Somesh Kumar Bhattacharya <somesh.kb at gmail.com> wrote:
> hello Eduardo Menendez,
>
> Thanks a lot for the PP ....................
> I will try with this and will report soon incase of any problems
> .......................
> ciao
>
> Somesh
>
>  On Dec 1, 2007 12:00 AM, Eduardo Ariel Menendez Proupin
> <eariel99 at gmail.com> wrote:
> > Hi,
> > Find attached one pseudo for Te. It is not Vanderbilt, but norm conserving
> RRKJ. I had made it ultrasoft before, but there is little difference, as
> long as the 4d electrons are in the core. Exchange correlation is PBE.
> > I use it for molecular dynamics setting ecutrho=30,ecutwfc=180, and
> tqr=-true.
> >
> > Eduardo Menendez
> >
> >
> >
> > 2007/11/30, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org>:
> >
> > > Send Pw_forum mailing list submissions to
> > >         pw_forum at pwscf.org
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > >          http://www.democritos.it/mailman/listinfo/pw_forum
> > > or, via email, send a message with subject or body 'help' to
> > >          pw_forum-request at pwscf.org
> > >
> > > You can reach the person managing the list at
> > >         pw_forum-owner at pwscf.org
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of Pw_forum digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > >    1. Te pseudopotentials (Somesh Kumar Bhattacharya)
> > >
> > >
> > > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Fri, 30 Nov 2007 11:03:03 +0530
> > > From: "Somesh Kumar Bhattacharya" <somesh.kb at gmail.com>
> > > Subject: [Pw_forum] Te pseudopotentials
> > > To: pw_forum at pwscf.org
> > > Message-ID:
> > >         <e0e40e0d0711292133s6b27af60k245fd5a9c9210ea8 at mail.gmail.com >
> > > Content-Type: text/plain; charset="iso-8859-1"
> > >
> > > Dear Users,
> > >
> > > I wish to do some calculations on CdTe clusters using PWSCF. For this I
> need
> > > Vanderbilt USPP  with PBE exchange correlation.
> > > For Cd it exist and I can get from the net. But for Te its not there.
> Can
> > > anyone please provide me with the required PP????
> > >
> > >
> > > Regards,
> > >
> > > Somesh
> > >
> > > SOMESH KR. BHATTACHARYA                   Ph.no.- (O)+91-
> 020-25692678-426
> > > JUNIOR RESEARCH FELLOW
> > > (M)+919921680580
> > > DEPT. OF PHYSICS
> > > UNIV. OF PUNE
> > > GANESHKHIND
> > > PUNE-411007
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL:
> http://www.democritos.it/pipermail/pw_forum/attachments/20071130/4ea06810/attachment.html
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> > >
> > > End of Pw_forum Digest, Vol 5, Issue 58
> > > ***************************************
> > >
> >
> >
> >
> > --
> > Eduardo Menendez
> >
> >
> > --
> > Eduardo Menendez
>
>
>
> --
> Somesh Kr. Bhattacharya
> Department of Physics,
> University of Pune,
> Ganeshkhind,
> Pune - 411007
> INDIA
> _______________________________________________
> 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 hqzhou at nju.edu.cn  Mon Dec  3 05:06:15 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Mon, 3 Dec 2007 12:06:15 +0800
Subject: [Pw_forum] how to continue my relax job
References: <aca2feb20711300336u4a92ee04u5c97cceac58ca894@mail.gmail.com>
Message-ID: <001701c83561$d9c5d520$1d00a8c0@solarflare>

Yuehua,

You should continue (restart) the relaxation with increased nstep.
Basically, you can set nsetup to a bigger value, say, 100-200 as
it has no harm because relaxation will stop as soon as convergence
is reached. In my case, I always set nstep to 200 for my complex
structrue.


Huiqun Zhou
@Earth Sciences, Nanjing University

  ----- Original Message ----- 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Friday, November 30, 2007 7:36 PM
  Subject: [Pw_forum] how to continue my relax job


  hi everyone here :
  i have another question about how to continue my relax job.for i set the 
  nstep is 50, too small ,and can not acheive convergence,and i want  to continue by adding the nstep,how to do with it ? 
  is it to add the restart option in input file?
  in general ,how many step i should to add?
  i wish your help 
  thank you ! 
  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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


  _______________________________________________
  Pw_forum mailing list
  Pw_forum at pwscf.org
  http://www.democritos.it/mailman/listinfo/pw_forum
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From njuxuyuehua at gmail.com  Mon Dec  3 08:12:58 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Mon, 3 Dec 2007 15:12:58 +0800
Subject: [Pw_forum] how to continue my relax job
In-Reply-To: <001701c83561$d9c5d520$1d00a8c0@solarflare>
References: <aca2feb20711300336u4a92ee04u5c97cceac58ca894@mail.gmail.com>
	<001701c83561$d9c5d520$1d00a8c0@solarflare>
Message-ID: <aca2feb20712022312x6d404e94w3b7ea56488776f35@mail.gmail.com>

thank Lorenzo Paulatto and Huiqun zhou .i will try it .

2007/12/3, Huiqun Zhou <hqzhou at nju.edu.cn>:
>
>  Yuehua,
>
> You should continue (restart) the relaxation with increased nstep.
> Basically, you can set nsetup to a bigger value, say, 100-200 as
> it has no harm because relaxation will stop as soon as convergence
> is reached. In my case, I always set nstep to 200 for my complex
> structrue.
>
>
> Huiqun Zhou
> @Earth Sciences, Nanjing University
>
>
>  ----- Original Message -----
> *From:* xu yuehua <njuxuyuehua at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Friday, November 30, 2007 7:36 PM
> *Subject:* [Pw_forum] how to continue my relax job
>
>
> hi everyone here :
> i have another question about how to continue my relax job.for i set the
> nstep is 50, too small ,and can not acheive convergence,and i want  to continue
> by adding the nstep,how to do with it ?
> is it to add the restart option in input file?
> in general ,how many step i should to add?
> i wish your help
> thank you !
> --
> Xu Yuehua
> physics Department of Nanjing university
> China
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Xu Yuehua
physics Department of Nanjing university
China
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From njuxuyuehua at gmail.com  Mon Dec  3 09:20:18 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Mon, 3 Dec 2007 16:20:18 +0800
Subject: [Pw_forum] a complex and old question about why the erengy is down
	when i enlarge one of the crystal lattice
Message-ID: <aca2feb20712030020hc593b03r4146275471669fa5@mail.gmail.com>

hi everyone:
my question is somewhat old ,i have seen a lot of related discussion in this
forum .but my results does not like previous instance.
i only want to relax c of crystal lattice ,and fixed c,computes it,and then
change it  ,compute it,and .....
i get the  E VS C tabular
so strange is that :

c               E
2.655     -137.78747
2.725     -137.7912
2.76      -137.79219
2.77       -137.79233
2.78      -137.79248
2.795      -137.79266
2.8         -137.7927
2.81       -137.79275
2.82       -137.79275
2.83       -137.79278
2.84       -137.79276
2.85       -137.79279
(1)the energy is down  before 2,81,and c=2.83 is like local minimum
,and then the energy is go on to down. the graph is smooth ,but   i can not
get the parabola shape .so the best relaxed structure is unkown to me.
  and  i saw many discuss about the down energy ,maybe the  ecutrho
issue.  but i am not sure .if ti is ,i should test the ecutrho?i post my
input file here:
&CONTROL
calculation  = "relax",
  prefix       = "xyh",
  pseudo_dir   = "/home/xyh/intel_espresso-3.2/pseudo",
  outdir       = "/raid/xyh/pwscf/tmp/",
  etot_conv_thr=1.D-5
  forc_conv_thr=1.D-4
  nstep=50
  tstress=.TRUE.
/
&SYSTEM
  ibrav     = 4,
  a=20,b=20,c=2.7950,cosab=-0.5,cosac=0,cosbc=0,
  nat       = 12,
  ntyp      = 2,
  ecutwfc   =29.9876 ,
  ecutrho   =200
/
&ELECTRONS
  conv_thr    = 1.D-9,
  mixing_beta = 0.2D0,
/
&IONS
  pot_extrapolation = "second_order",
  wfc_extrapolation = "second_order",
/
 ATOMIC_SPECIES
H  1.0  H.pbe-van_bm.UPF
O 15.999 O.pbe-van_bm.UPF
ATOMIC_POSITIONS { crystal }
H  0.0373836515057430  0.9503896146857272  0.0102606085503574
H  0.1115317646909714  0.9930799089192295  0.3344160938275307
H  0.0789318950169224  0.0718359337861800  0.9884868039481935
H  0.0724243415282819  0.1328116898677112  0.6645236821235255
H  0.9626484865634389  0.0496365043168296  0.0101367101334339
H  0.8884876867936907  0.0069387333102180  0.3342097796899214
H  0.9210924986163674  0.9281832378776828  0.9882981504770443
H  0.9276176392628244  0.8672101853812219  0.6643346513014633
O  0.0926597580972745  0.9929556282114975
......


..
(2)and another question is although i can not get the lowest erengy,but i
can get the parabola of  the stress. maybe someone the stress is not
consistent with energy,for i only want to    know  which  structure is best
,so the exactly stress is not so import for me, i only want to know the
trend .in this point,whether i can rely on the stress to determine the best
structure.

i need your help.
thanks
 --
Xu Yuehua
physics Department of Nanjing university
China
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From hande at newton.physics.metu.edu.tr  Mon Dec  3 09:33:03 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Mon, 3 Dec 2007 10:33:03 +0200 (EET)
Subject: [Pw_forum] a complex and old question about why the erengy is
 down when i enlarge one of the crystal lattice
In-Reply-To: <aca2feb20712030020hc593b03r4146275471669fa5@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0712031027160.4163-100000@newton.physics.metu.edu.tr>

Dear Xu Yuehua,

> hi everyone:
> my question is somewhat old ,i have seen a lot of related discussion in this
> forum .but my results does not like previous instance.
> i only want to relax c of crystal lattice ,and fixed c,computes it,and then
> change it  ,compute it,and .....
> i get the  E VS C tabular


It seems like you have explored only one side of the minimum making your
plot lopsided. In order to get a good fit, you need to go to c values that
are a bit larger than 2.85. As it is your polynomial fit will be rather
unhealthy. Along the same lines, once you have gone further towards larger
c, you could discard the two smallest c, namely 2.655 and 2.725. To make
the curve smoother try a larger ecutwfc and a larger ecutrho. I would
probably go for 35 Ryd and 350 Ryd. 


> (2)and another question is although i can not get the lowest erengy,but i
> can get the parabola of  the stress. maybe someone the stress is not
> consistent with energy,for i only want to    know  which  structure is best
> ,so the exactly stress is not so import for me, i only want to know the
> trend .in this point,whether i can rely on the stress to determine the best
> structure.

I would still try to fix the energy curve. Not only does this give you the
lowest energy of the structure, a smooth curve is at the same time a good
indication that your calculations parameters such as ecutwfc are good.


Best of luck,
Hande

-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande


From njuxuyuehua at gmail.com  Mon Dec  3 10:20:00 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Mon, 3 Dec 2007 17:20:00 +0800
Subject: [Pw_forum] a complex and old question about why the erengy is
	down when i enlarge one of the crystal lattice
In-Reply-To: <Pine.LNX.4.44.0712031027160.4163-100000@newton.physics.metu.edu.tr>
References: <aca2feb20712030020hc593b03r4146275471669fa5@mail.gmail.com>
	<Pine.LNX.4.44.0712031027160.4163-100000@newton.physics.metu.edu.tr>
Message-ID: <aca2feb20712030120p6abfc83dkb5df066b4c1de2b@mail.gmail.com>

thank hande for your advice .
but i am still puzzled below:
(1) last time ,i saw a titled " scan  the lattice "discussion ,and you could
find it in forum,they said:
Basically, as you enalarge your unit cell, your brillouin zone shrinks,
and at constant cutoff it means that more lattice vectors (i.e. plane
waves) enter into the fixed cutoff sphere. More plane waves means a
systematically larger basis set (this is one of the good things
of plane waves, it's easy to make the basis set more and more complete -
a nightmare in Gaussian), and, variationally, a lower energy. You see in
fact your energy drop going to the left.

Check then what is the number of plane waves for each of your
calculations, but most likely the wfc cutoff is the culprit

so i feel if i keep the encut fixed,and enlarge the lattice ,the more number
of plane waves will enter into the calculation ,and will get the lower
energy.  i do not understand what is the relationship between more plane
waves and a lower energy .
and just now you told me to set bigger encut and ..,seems opposite  to the
above discussion .
maybe my understanding is wrong .

i need your help .
thanks in advance
2007/12/3, Hande Ustunel <hande at newton.physics.metu.edu.tr>:
>
> Dear Xu Yuehua,
>
> > hi everyone:
> > my question is somewhat old ,i have seen a lot of related discussion in
> this
> > forum .but my results does not like previous instance.
> > i only want to relax c of crystal lattice ,and fixed c,computes it,and
> then
> > change it  ,compute it,and .....
> > i get the  E VS C tabular
>
>
> It seems like you have explored only one side of the minimum making your
> plot lopsided. In order to get a good fit, you need to go to c values that
> are a bit larger than 2.85. As it is your polynomial fit will be rather
> unhealthy. Along the same lines, once you have gone further towards larger
> c, you could discard the two smallest c, namely 2.655 and 2.725. To make
> the curve smoother try a larger ecutwfc and a larger ecutrho. I would
> probably go for 35 Ryd and 350 Ryd.
>
>
> > (2)and another question is although i can not get the lowest erengy,but
> i
> > can get the parabola of  the stress. maybe someone the stress is not
> > consistent with energy,for i only want to    know  which  structure is
> best
> > ,so the exactly stress is not so import for me, i only want to know the
> > trend .in this point,whether i can rely on the stress to determine the
> best
> > structure.
>
> I would still try to fix the energy curve. Not only does this give you the
> lowest energy of the structure, a smooth curve is at the same time a good
> indication that your calculations parameters such as ecutwfc are good.
>
>
> Best of luck,
> Hande
>
> --
> Hande Ustunel
> Department of Physics
> Office 439
> Middle East Technical University
> Ankara 06531, Turkey
> Tel : +90 312 210 3264
> http://www.physics.metu.edu.tr/~hande
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From bnrj.rudra at yahoo.com  Mon Dec  3 10:52:55 2007
From: bnrj.rudra at yahoo.com (Rudra Banerjee)
Date: Mon, 3 Dec 2007 15:22:55 +0530 (IST)
Subject: [Pw_forum] (no subject)
Message-ID: <772663.48432.qm@web94114.mail.in2.yahoo.com>

hello friends,
i am facing a problem. i am trying to relax my system,with input file
&control
    calculation='relax'
    pseudo_dir = '/home/rudra/espresso_work/pseudo/',
    restart_mode = 'from_scratch' ,
    outdir='.'
    title='Relax Water Hexamer Book Structure'
    prefix='book'
    tprnfor=.true., 
    tstress=.true.
    nstep=100,
 /
 &system
    ibrav=  1,
    celldm(1) = 24.,
    nat=18, 
    ntyp= 2,
    ecutwfc = 60.0,
    ecutrho = 180.0 ,
    nbnd= 52,
    xc_type = 'BLYP',
 /
  &electrons
   conv_thr = 1.d-3 
 /
  &ions
   ion_dynamics = 'bfgs' ,
   upscale = 30.D0 ,
   trust_radius_max = 5.0D-1 ,
   trust_radius_min = 1.0D-10 ,
 /    
ATOMIC_SPECIES
 O 16.0d0 O.BLYP.UPF
 H  1.0d0 H.fpmd.UPF
ATOMIC_POSITIONS (bohr)
O       -3.765850089   2.604262152   2.619442162
O        3.257666971   0.556462826   0.567981255
O        0.721513716   5.028138562   1.453740093
O        2.459939568  -1.173597129  -4.376727719
O       -0.795639896  -4.762757998  -2.273327611
O       -1..446214713  -2.020509104   2.240245088
H       -5.130209799   3.094215504   1.480725193
H       -2.297814319   3.717759149   2.145327713
H        2.001314966  -0.548297328   1.386980992
H        3.171211589   0.032349699  -1.239918611
H        1.783161893   3.503054113   1.019956064
H        0.911072560   6.158083552   0.008560339
H        1.268754221  -2.551175782  -3.887721179
H        3.858660869  -2.043651487  -5.199877530
H       -2.411497662  -5.196233584  -3.045652507
H       -1.249081673  -3.902600390  -0.661327634
H       -2.452970050  -0.404000526   2.341480766
H       -1.721709152  -2.854164227   3.859806125
K_POINTS {automatic}
2 2 2 0 0 0 
whivh is returnning the error:
resetting bfgs history
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from bfgs : error #         1
     bfgs history already reset at previous step
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
2
i did checked the forum archive and saw that it may  be caused due to high force convergence threshold (which i was giving it in previous calculati, only to return with the same error). Now,i relied on the default value and stiil its comming.......any idea why?
------
Rudra
Have a Nice Time
http://www.bose.res.in/~rudra
Please, if possible, don't  send me MS Word or PowerPoint attachments        
Why?See:  http://www.gnu.org/philosophy/no-word-attachments.html






      Get the freedom to save as many mails as you wish. To know how, go to http://help.yahoo.com/l/in/yahoo/mail/yahoomail/tools/tools-08.html
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From katalin.gaal-nagy at physik.uni-regensburg.de  Mon Dec  3 11:39:14 2007
From: katalin.gaal-nagy at physik.uni-regensburg.de (Katalin Gaal-Nagy)
Date: Mon, 3 Dec 2007 11:39:14 +0100 (CET)
Subject: [Pw_forum] a complex and old question about why the erengy is
 down when i enlarge one of the crystal lattice
In-Reply-To: <aca2feb20712030120p6abfc83dkb5df066b4c1de2b@mail.gmail.com>
References: <aca2feb20712030020hc593b03r4146275471669fa5@mail.gmail.com>
	<Pine.LNX.4.44.0712031027160.4163-100000@newton.physics.metu.edu.tr>
	<aca2feb20712030120p6abfc83dkb5df066b4c1de2b@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0712031120560.13891@pcph099.physik.uni-regensburg.de>

Dear Yuehua,

it is true that the ecut gives you the number of plane waves used in the 
calculation and a test of ecut (fixed lattice, various values of ecut) 
gives you the resolution of the energy in your calculation. More plane 
waves (larger ecut) lowers the energy of your system. The variation of the 
number of plane waves with a change of the volume at fixed ecut was 
discussed in PRB 52, 8160 (1995). There, also some corrections to the 
total energy with respect to the change of the number of plane waves are 
suggested.  Of course, if you have a calculation which is converged with 
respect to ecut, these errors are very small.

So, in order to relax your system you first should test the convergence 
with respect to ecut (and the number of k) and with these values you 
should relax the system with respect to c/a and the volume of the unit 
cell. I suggest to relax the c/a for a fixed volume in order to avoid the 
spurious variations with respect to the number of plane waves by looking 
at Etot(c/a). This you should do for every volume you consider. Having the 
volumes with the correct c/a fixed, you can look at Etot(V) in order to 
get the relaxed system.

About the influence of ecutrho I cannot say anything, since it never 
played a significant role in my calculations. But maybe someone else could 
give further informations.

Good luck,
Katalin


,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
, >>>>>>>             Katalin Gaal-Nagy              <<<<<<< ,
,                      Phys.Dept./INFM                       ,
,                    University of Milan                     ,
,                      Via Celoria 16                        ,
,                     +39 02 50317377                        ,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
, >>>>>>> katalin.gaal-nagy at physik.uni-regensburg.de <<<<<<< ,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
, >>>>>>>   Don't dream your life, live your dream   <<<<<<< ,
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,


> thank hande for your advice .
> but i am still puzzled below:
> (1) last time ,i saw a titled " scan  the lattice "discussion ,and you could
> find it in forum,they said:
> Basically, as you enalarge your unit cell, your brillouin zone shrinks,
> and at constant cutoff it means that more lattice vectors (i.e. plane
> waves) enter into the fixed cutoff sphere. More plane waves means a
> systematically larger basis set (this is one of the good things
> of plane waves, it's easy to make the basis set more and more complete -
> a nightmare in Gaussian), and, variationally, a lower energy. You see in
> fact your energy drop going to the left.
>
> Check then what is the number of plane waves for each of your
> calculations, but most likely the wfc cutoff is the culprit
>
> so i feel if i keep the encut fixed,and enlarge the lattice ,the more number
> of plane waves will enter into the calculation ,and will get the lower
> energy.  i do not understand what is the relationship between more plane
> waves and a lower energy .
> and just now you told me to set bigger encut and ..,seems opposite  to the
> above discussion .
> maybe my understanding is wrong .
>
> i need your help .
> thanks in advance
> 2007/12/3, Hande Ustunel <hande at newton.physics.metu.edu.tr>:
>>

From lanhaiping at gmail.com  Mon Dec  3 11:46:42 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 3 Dec 2007 18:46:42 +0800
Subject: [Pw_forum] (no subject)
In-Reply-To: <772663.48432.qm@web94114.mail.in2.yahoo.com>
References: <772663.48432.qm@web94114.mail.in2.yahoo.com>
Message-ID: <c92002fa0712030246k5c2a44f1j3c3513c9c395b234@mail.gmail.com>

the convergence thread in your script is
  conv_thr = 1.d-3
which is too large  to give any result reliable.
The default value is 1.0D-6..

On Dec 3, 2007 5:52 PM, Rudra Banerjee <bnrj.rudra at yahoo.com> wrote:

> hello friends,
> i am facing a problem. i am trying to relax my system,with input file
> &control
>     calculation='relax'
>     pseudo_dir = '/home/rudra/espresso_work/pseudo/',
>     restart_mode = 'from_scratch' ,
>     outdir='.'
>     title='Relax Water Hexamer Book Structure'
>     prefix='book'
>     tprnfor=.true.,
>     tstress=.true.
>     nstep=100,
>  /
>  &system
>     ibrav=  1,
>     celldm(1) = 24.,
>     nat=18,
>     ntyp= 2,
>     ecutwfc = 60.0,
>     ecutrho = 180.0 ,
>     nbnd= 52,
>     xc_type = 'BLYP',
>  /
>   &electrons
>    conv_thr = 1.d-3
>  /
>   &ions
>    ion_dynamics = 'bfgs' ,
>    upscale = 30.D0 ,
>    trust_radius_max = 5.0D-1 ,
>    trust_radius_min = 1.0D-10 ,
>  /
> ATOMIC_SPECIES
>  O 16.0d0 O.BLYP.UPF
>  H  1.0d0 H.fpmd.UPF
> ATOMIC_POSITIONS (bohr)
> O       -3.765850089   2.604262152   2.619442162
> O        3..257666971   0.556462826   0.567981255
> O        0.721513716   5.028138562   1.453740093
> O        2.459939568  -1.173597129  -4.376727719
> O       -0.795639896  -4.762757998  -2.273327611
> O       -1.446214713  -2.020509104   2.240245088
> H       -5.130209799   3.094215504   1.480725193
> H       -2.297814319   3.717759149   2.145327713
> H        2.001314966  -0.548297328   1.386980992
> H        3.171211589   0.032349699  -1.239918611
> H        1.783161893   3.503054113   1.019956064
> H        0.911072560   6.158083552   0.008560339
> H        1.268754221  -2.551175782  -3.887721179
> H        3.858660869  -2.043651487  -5.199877530
> H       -2.411497662  -5.196233584  -3.045652507
> H       -1.249081673  -3.902600390  -0.661327634
> H       -2.452970050  -0.404000526   2.341480766
> H       -1.721709152  -2.854164227   3.859806125
> K_POINTS {automatic}
> 2 2 2 0 0 0
> whivh is returnning the error:
> resetting bfgs history
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from bfgs : error #         1
>      bfgs history already reset at previous step
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      stopping ...
> 2
> i did checked the forum archive and saw that it may  be caused due to high
> force convergence threshold (which i was giving it in previous calculati,
> only to return with the same error). Now,i relied on the default value and
> stiil its comming......any idea why?
> ------
> Rudra
> Have a Nice Time
> http://www.bose.res.in/~rudra <http://www.bose.res.in/%7Erudra>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why?See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
>
> ------------------------------
> Meet people who discuss and share your passions. Join them now.<http://in.rd.yahoo.com/tagline_groups_7/*http://in.promos.yahoo.com/groups>
>
> _______________________________________________
> 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  Mon Dec  3 16:30:21 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 3 Dec 2007 10:30:21 -0500
Subject: [Pw_forum] (no subject)
In-Reply-To: <c92002fa0712030246k5c2a44f1j3c3513c9c395b234@mail.gmail.com>
References: <772663.48432.qm@web94114.mail.in2.yahoo.com>
	<c92002fa0712030246k5c2a44f1j3c3513c9c395b234@mail.gmail.com>
Message-ID: <7b6913e90712030730v150c9586j50b492505d584f7a@mail.gmail.com>

On Dec 3, 2007 5:46 AM, lan haiping <lanhaiping at gmail.com> wrote:
>
> the convergence thread in your script is
>
>   conv_thr = 1.d-3
> which is too large  to give any result reliable.
> The default value is 1.0D-6..
>

to elaborate a little bit on this:

to converge a geometry well, you need accurate forces.
to get accurate forces you need a well converged wavefunction
(=> small conv_thr in &electrons). you also have to converge
your basis set (ecutwfc) with respect to forces. now the latter
depends on the pseudopotentials, that you are using and for
norm-conserving pseudopotentials for oxygen a cutoff of 60ry
is too small. for CP dynamics people have gotten away with 70ry
for a long time, but there is evidence that 85ry is much more
appropriate and for very accurate geometries you may need over
100ry. finally, as mentioned before, for norm-conserving pseudopotentials,
you should stick with the regular ecutwfc/ecutrho ratio of 4. this
is twice as important for geometry optimizations, since any other
grid ratio will introduce additional "ripples" in the 3d density grid
and thus make convergece more difficult.

hope this helps,
    axel.

[...]

>
> --
> 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
>
>



-- 
=======================================================================
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 vietbacchemist at gmail.com  Tue Dec  4 05:12:03 2007
From: vietbacchemist at gmail.com (Viet Bac)
Date: Tue, 4 Dec 2007 13:12:03 +0900
Subject: [Pw_forum] Problem with q2r.x running
Message-ID: <ea64856c0712032012hf72ef8elf1f785bc46063880@mail.gmail.com>

Dear QE users,
I am doing EPC calculation for supercell and I got error with q2r.x when I
want to do q2r.x to bring force constants and el-phon coefficients (results
from ph.x)  to real space. My supercell includes ibraiv =0, and I search
somewhere in this forum, Dr. Stefano had stated this problem has solved
already.
So anybody can help me to explain this error? (Is there any problem with
a2Fq2r.* data??)
I attached the error

 /../espresso-3.2.3/bin/q2r.x <q2r.in> q2r.out
forrtl: severe (59): list-directed I/O syntax error, unit 51, file
/../a2Fq2r.51
Image              PC                Routine            Line
Source
q2r.x              00000000007AAE06  Unknown               Unknown  Unknown
q2r.x              00000000007AA002  Unknown               Unknown  Unknown
q2r.x              0000000000766026  Unknown               Unknown  Unknown
q2r.x              0000000000722EBE  Unknown               Unknown  Unknown
.....................

And I use K-points grid 1*1*40 in scf calculation and q-points grid 1*1*10.
My scf Input:
 &CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/root/tmp' ,
                  pseudo_dir = '/usr/local/ESPRESSO_S/espresso-3.2.3/pseudo/'
,
                      prefix = 'al4d_elph' ,
 /
 &SYSTEM
                       ibrav = 0,
                   celldm(1) = 40,
                         nat = 4,
                        ntyp = 1,
                     ecutwfc = 25.D0 ,
                 occupations = 'smearing' ,
                     degauss = 0.05 ,
                    smearing = 'methfessel-paxton' ,
                      la2F = .true.
 /
 &ELECTRONS
                    conv_thr = 1.D-10 ,
                 mixing_beta = 0.7D0 ,
 /
CELL_PARAMETERS alat
   0.999310440   0.000000000   0.000000000
   0.000000000   0.999469296   0.000001912
   0.000000000   0.000000438   0.228398270
ATOMIC_SPECIES
   Al   26.98000  Al.vbc.UPF
ATOMIC_POSITIONS angstrom
Al       0.000000000   2.292015084   1.208608723
Al       0.000000000  -0.051852693  -0.000016750
Al       0.000000000  -0.051739937   2.417248391
Al       0.000000000   2.292076740   3.625876674
K_POINTS automatic
  1 1 40   0 0 0


I appreciated any help and suggest,

Bac

------------------------------
Phung Viet Bac
Division of Mathematical and Physical Science,
Graduate School of Natural Science and Technology,
Kanazawa University,
Kakuma, Kanazawa 920-1192, JAPAN
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From raamesh123 at rediffmail.com  Tue Dec  4 09:59:14 2007
From: raamesh123 at rediffmail.com (ramesh  kumar)
Date: 4 Dec 2007 08:59:14 -0000
Subject: [Pw_forum] installation problem
Message-ID: <20071204085914.1528.qmail@f5mail-237-201.rediffmail.com>

  
Dear friends

make all says 

comments like this 

gfortran: -lfftw: linker input file unused because linking not done
gfortran -O3 -x f95-cpp-input -D__FFTW -I../include  -lfftw -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH  -I../CPV -c vloc_psi.f90
gfortran: -lfftw: linker input file unused because linking not done
gfortran -O3 -x f95-cpp-input -D__FFTW -I../include  -lfftw -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH  -I../CPV -c vpack.f90
gfortran: -lfftw: linker input file unused because linking not done
gfortran -O3 -x f95-cpp-input -D__FFTW -I../include  -lfftw -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH  -I../CPV -c w0gauss.f90
gfortran: -lfftw: linker input file unused because linking not done
gfortran -O3 -x f95-cpp-input -D__FFTW -I../include  -lfftw -I./  -I../Modules  -I../iotk/src -I../PW  -I../PH  -I../CPV -c w1gauss.f90


please help me in this regard

thanks

with regards
ramesh
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From giannozz at nest.sns.it  Tue Dec  4 13:14:07 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 4 Dec 2007 13:14:07 +0100
Subject: [Pw_forum] Problem with q2r.x running
In-Reply-To: <ea64856c0712032012hf72ef8elf1f785bc46063880@mail.gmail.com>
References: <ea64856c0712032012hf72ef8elf1f785bc46063880@mail.gmail.com>
Message-ID: <1E9BFC47-CB84-4718-8DCC-7B49BCFC6D39@nest.sns.it>


On Dec 4, 2007, at 5:12 , Viet Bac wrote:

> (Is there any problem with a2Fq2r.* data??)

sure there is one, and it is explicitle stated in
the error message:

> forrtl: severe (59): list-directed I/O syntax error, unit 51,  
> file /../a2Fq2r.51


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 nest.sns.it  Tue Dec  4 13:14:27 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 4 Dec 2007 13:14:27 +0100
Subject: [Pw_forum] installation problem
In-Reply-To: <20071204085914.1528.qmail@f5mail-237-201.rediffmail.com>
References: <20071204085914.1528.qmail@f5mail-237-201.rediffmail.com>
Message-ID: <66D7D27E-A7C5-4CF0-A499-7C501EA5E6AC@nest.sns.it>


On Dec 4, 2007, at 9:59 , ramesh kumar wrote:

> make all says comments like this
>
> gfortran -O3 -x f95-cpp-input -D__FFTW -I../include  -lfftw -I./  - 
> I../Modules  -I../iotk/src -I../PW  -I../PH  -I../CPV -c vloc_psi.f90
> gfortran: -lfftw: linker input file unused because linking not done
>

from make.sys:
---
# 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
---
you added -lfftw to IFLAGS. Do not know the difference between
"include files" and libraries? if not, please stick to internal FFTW
libraries and don't try to mess up with the make.sys file.

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 elena.cannuccia at roma2.infn.it  Tue Dec  4 14:47:55 2007
From: elena.cannuccia at roma2.infn.it (Elena Cannuccia)
Date: Tue, 4 Dec 2007 14:47:55 +0100 (CET)
Subject: [Pw_forum] XD1 is on again
In-Reply-To: <Pine.LNX.4.64.0712031120560.13891@pcph099.physik.uni-regensburg.de>
References: <aca2feb20712030020hc593b03r4146275471669fa5@mail.gmail.com>
	<Pine.LNX.4.44.0712031027160.4163-100000@newton.physics.metu.edu.tr>
	<aca2feb20712030120p6abfc83dkb5df066b4c1de2b@mail.gmail.com>
	<Pine.LNX.4.64.0712031120560.13891@pcph099.physik.uni-regensburg.de>
Message-ID: <1637.151.49.121.44.1196776075.squirrel@151.49.121.44>


Hi Katalin,

I submitted 3 jobs on xd1 few hours ago, because xd1 can be used again now.

I spoke to Olivia this morning. I told her the problem we had for xd1, she
told me to use sp5 if necessary. So I'm going to finish my time evolutions on
oxidized flavin and after to decide what to do. (Don't worry, I don't need too
many hours).

She also told me that maybe you shouldn't do a tddft calculation with a
radius=8ang, a casida calculation is enough. (But it's better if you speak to
her.) If you'll have to do only a casida calculation, we have hours enough.

see you later

bye bye


-----------------------------------------------------------------
My lessons:

On Monday:   from 14:30 to 18:00
On Tuesday:  from 9:15  to 10:50 and from 14:30 to 16:00
On Thursday: from 14:30 to 17:30
-----------------------------------------------------------------

From elena.cannuccia at roma2.infn.it  Tue Dec  4 15:23:40 2007
From: elena.cannuccia at roma2.infn.it (Elena Cannuccia)
Date: Tue, 4 Dec 2007 15:23:40 +0100 (CET)
Subject: [Pw_forum] a complex and old question about why the erengy is
 down when i enlarge one of the crystal lattice
In-Reply-To: <Pine.LNX.4.64.0712031120560.13891@pcph099.physik.uni-regensburg.de>
References: <aca2feb20712030020hc593b03r4146275471669fa5@mail.gmail.com>
	<Pine.LNX.4.44.0712031027160.4163-100000@newton.physics.metu.edu.tr>
	<aca2feb20712030120p6abfc83dkb5df066b4c1de2b@mail.gmail.com>
	<Pine.LNX.4.64.0712031120560.13891@pcph099.physik.uni-regensburg.de>
Message-ID: <33608.141.108.250.13.1196778220.squirrel@141.108.250.13>

Sorry for my previous mail...
I didn't want to send it to everyone....
Sorry again...




> Dear Yuehua,
>
> it is true that the ecut gives you the number of plane waves used in the
> calculation and a test of ecut (fixed lattice, various values of ecut)
> gives you the resolution of the energy in your calculation. More plane
> waves (larger ecut) lowers the energy of your system. The variation of the
> number of plane waves with a change of the volume at fixed ecut was
> discussed in PRB 52, 8160 (1995). There, also some corrections to the
> total energy with respect to the change of the number of plane waves are
> suggested.  Of course, if you have a calculation which is converged with
> respect to ecut, these errors are very small.
>
> So, in order to relax your system you first should test the convergence
> with respect to ecut (and the number of k) and with these values you
> should relax the system with respect to c/a and the volume of the unit
> cell. I suggest to relax the c/a for a fixed volume in order to avoid the
> spurious variations with respect to the number of plane waves by looking
> at Etot(c/a). This you should do for every volume you consider. Having the
> volumes with the correct c/a fixed, you can look at Etot(V) in order to
> get the relaxed system.
>
> About the influence of ecutrho I cannot say anything, since it never
> played a significant role in my calculations. But maybe someone else could
> give further informations.
>
> Good luck,
> Katalin
>
>
> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
> , >>>>>>>             Katalin Gaal-Nagy              <<<<<<< ,
> ,                      Phys.Dept./INFM                       ,
> ,                    University of Milan                     ,
> ,                      Via Celoria 16                        ,
> ,                     +39 02 50317377                        ,
> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
> , >>>>>>> katalin.gaal-nagy at physik.uni-regensburg.de <<<<<<< ,
> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
> , >>>>>>>   Don't dream your life, live your dream   <<<<<<< ,
> ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
>
>
>> thank hande for your advice .
>> but i am still puzzled below:
>> (1) last time ,i saw a titled " scan  the lattice "discussion ,and you could
>> find it in forum,they said:
>> Basically, as you enalarge your unit cell, your brillouin zone shrinks,
>> and at constant cutoff it means that more lattice vectors (i.e. plane
>> waves) enter into the fixed cutoff sphere. More plane waves means a
>> systematically larger basis set (this is one of the good things
>> of plane waves, it's easy to make the basis set more and more complete -
>> a nightmare in Gaussian), and, variationally, a lower energy. You see in
>> fact your energy drop going to the left.
>>
>> Check then what is the number of plane waves for each of your
>> calculations, but most likely the wfc cutoff is the culprit
>>
>> so i feel if i keep the encut fixed,and enlarge the lattice ,the more number
>> of plane waves will enter into the calculation ,and will get the lower
>> energy.  i do not understand what is the relationship between more plane
>> waves and a lower energy .
>> and just now you told me to set bigger encut and ..,seems opposite  to the
>> above discussion .
>> maybe my understanding is wrong .
>>
>> i need your help .
>> thanks in advance
>> 2007/12/3, Hande Ustunel <hande at newton.physics.metu.edu.tr>:
>>>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>


From glevita at units.it  Tue Dec  4 15:57:28 2007
From: glevita at units.it (glevita at units.it)
Date: Tue, 04 Dec 2007 15:57:28 +0100
Subject: [Pw_forum] Questions about plotting
In-Reply-To: <AC903C05-B191-4D2A-89EB-6254DD62A21E@nest.sns.it>
References: <BLU120-W4022974564AE92E34ADD64AA700@phx.gbl>
	<20071129190112.oedjh66j2g8o48cw@webmail.units.it>
	<1196420714.2623.5.camel@localhost.localdomain>
	<20071130161230.40gbd9j093s4cg40@webmail.units.it>
	<AC903C05-B191-4D2A-89EB-6254DD62A21E@nest.sns.it>
Message-ID: <20071204155728.wu8wiebh6b0gww4s@webmail.units.it>


Dear Paolo and Tone, thank you very much for your suggestions.
I verified that by using a serial version of the code, the linear  
projection of the charge density is generated correctly. Good news for  
that matters, then.
The only problem is that now I tried to do the same for the ILDOS in a  
certain energy range, and the pp program stops with

  IOS = 36
   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      from davcio : error #        10
      i/o error in davcio
   
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
      stopping ...

My obvious guess is that it is not possible for a serial PP to read  
the numerous  temporary files generated by a parallel PW version.  
However, how is it possible that the charge density is actually well  
computed, and the ILDOS is not?
I now try searching the forum archive for some advices...
Thanks,
  Giacomo


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

>
> On Nov 30, 2007, at 16:12 , glevita at units.it wrote:
>
>> In the INPUT_PP example it is reported that the output_format
>> selection is ignored when 1D plots are chosen. (moreover, the
>> output_format= 3 option is reported to be suited also to 1D Xcrysden).
>> In fact, I failed both when output_format was 0 and 3, and when iflag
>> was either 0 or 1. No plot files were generated, even if the first PP
>> output file was OK.
>
> there are way too many options in the postprocessing codes to
> keep track of all of them. If it works in the serial case, it is for
> sure a problem of parallel execution.
>
>> I used both a 3.2.2 version of Espresso and a 3.0 one.
>
> it is not unlikely that your problem may have been solved meanwhile.
> See http://www.democritos.it:8888/O-sesame/chngview?cn=5321
> and http://www.democritos.it:8888/O-sesame/chngview?cn=4894
>
> 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 ezadshojaee at hotmail.com  Tue Dec  4 16:15:49 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Tue, 4 Dec 2007 15:15:49 +0000
Subject: [Pw_forum] about Fermi Energy shift in periodic (q=0) perturbations
Message-ID: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>


Hi
can anyone refer me to some speciefic references about how and why perodic perturbations(q=0) shift Fermi Energy in metals(in detail)?
Thanx  
_________________________________________________________________
Explore the seven wonders of the world
http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE
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From marzari at MIT.EDU  Tue Dec  4 19:26:31 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 04 Dec 2007 13:26:31 -0500
Subject: [Pw_forum] about Fermi Energy shift in periodic (q=0)
	perturbations
In-Reply-To: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>
References: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>
Message-ID: <47559BD7.4040104@mit.edu>


Ezad Shojaee wrote:
> Hi
> can anyone refer me to some speciefic references about how and 
> why perodic perturbations(q=0) shift Fermi Energy in metals(in detail)?
> Thanx 


Probably this is a good start:
http://arxiv.org/abs/0709.4647


			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 pqshen at yahoo.com  Tue Dec  4 22:13:46 2007
From: pqshen at yahoo.com (Peiqing Shen)
Date: Tue, 4 Dec 2007 13:13:46 -0800 (PST)
Subject: [Pw_forum] CRASH when running example18
Message-ID: <770551.44077.qm@web43143.mail.sp1.yahoo.com>

Hi,

After compiling the PWscf package, I tried to run all
executables one by one. But I got only PW.X to run
without any problem. When I tried to run example18 (in
parallel version), I got the following message:

/bigdisk/staff/pshen/esp3_2_3/espresso-3.2.3/examples/example18
: starting

This example shows how to use cp.x to perform
molecular dynamics
simulation of SiO2.

  executables directory:
/bigdisk/staff/pshen/esp3_2_3/espresso-3.2.3/bin
  pseudo directory:     
/bigdisk/staff/pshen/esp3_2_3/espresso-3.2.3/pseudo
  temporary directory:   /home/staff/pshen/tmp
  checking that needed directories and files exist...
done

  running cp.x as: mpirun -np 1
/bigdisk/staff/pshen/esp3_2_3/espresso-3.2.3/bin
/cp.x 

  cleaning /home/staff/pshen/tmp... done
  running the calculation with fixed ions...FORTRAN
STOP
 done
  running the calculation with fixed ions,
restart...###########################
################################################################################
#############
# UNRECOVERABLE ERROR (ierr=1)
# ERROR IN: iotk_scan_dat_aux (iotk_dat.spp:461)
# CVS Revision: 1.3 
# Missing dat
################################################################################
########################################
[0] MPI Abort by user Aborting program !
[0] Aborting program!
 done
  running the variable-cell calculation...[0] MPI
Abort by user Aborting program
 !
[0] Aborting program!
 done
  running the variable-cell calculation, restart...[0]
MPI Abort by user Abortin
g program !
[0] Aborting program!
 done

/bigdisk/staff/pshen/esp3_2_3/espresso-3.2.3/examples/example18
: done

I go to  results directory, the the file 'CRASH' have
the following message:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     task #         0
     from cp_read_cell : error #         1
     cannot open restart file for reading:
/home/staff/pshen/tmp/cp_93.save/data-file.xml

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

It's true that there is no file in the directory
/home/staff/pshen/tmp/cp_93.save

Could any one let me know what happened when
restarting CP.X?

THanks a lot.

Peiqing Shen
CTSPS & Dept. of Physics
Clark Atlanta University



      ____________________________________________________________________________________
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From jdogbe at gmail.com  Wed Dec  5 05:22:08 2007
From: jdogbe at gmail.com (John K. Dogbe)
Date: Tue, 04 Dec 2007 23:22:08 -0500
Subject: [Pw_forum] Help
Message-ID: <47562770.7080608@gmail.com>

Hi,

Could anyone kindly help me understand the following errors I got during 
"make all" on SGI Origin 200?  I'm using SGI compiler and I have 
compiled fftw2.1.5 for use. Could there be a problem with my fftw build?

 use iotk_attr_interf
                                 ^
f90-1108 mfef90: ERROR IOTK_COPY_DAT_AUX_X, File = iotk_misc.F90, Line = 341, Column = 34 
  The type of the actual argument, "Cray character pointer", does not match "CHARACTER", the type of the dummy argument.

f90: MIPSpro Fortran 90 Version 7.2.1  (f51) Tue Dec  4, 2007  23:07:52
f90: 689 source lines
f90: 1 Error(s), 0 Warning(s), 0 Other message(s), 0 ANSI(s)
*** Error code 2 (bu21)
*** Error code 1 (bu21)
*** Error code 1 (bu21)

thank you.
John.

- 
============================================================
John K. Dogbe, Visiting Assistant Professor
Barton College, Dept. of Science & Mathematics
400 Atlantic Christian College Dr. NE, Wilson,NC 27893-2575
Tel.: (252) 399-6471, Fax.: (252) 399-6465         ============================================================
**The first is not necessarily the Leader**

        "If I have spoken evil, bear witness of the evil:
                but if well, why smitest thou me?"
                                -- Jesus Christ (John, 18:23)


From gaoguoying at gmail.com  Wed Dec  5 08:05:32 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Wed, 5 Dec 2007 15:05:32 +0800
Subject: [Pw_forum] question on q2r.f90
Message-ID: <6234c0c60712042305u51ef13cbmfef8bd7df7be1a3b@mail.gmail.com>

Dear everyone,
      When I read the routine q2r.f90 given in the pwtools directory,
I find the following lines:
  %%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
        lq = .true.
        do ipol=1,3
           xq = 0.0
           do icar=1,3
              xq = xq + at(icar,ipol) * q(icar,nq) * nr(ipol)
           end do
           lq = lq .and. (abs(nint(xq) - xq) .lt. eps)
           iq = nint(xq)
           !
           m(ipol)= mod(iq,nr(ipol)) + 1
           if (m(ipol) .lt. 1) m(ipol) = m(ipol) + nr(ipol)
        end do
        if (.not.lq) call errore('init','q not allowed',1)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
I know the parameters at(icar, ipol) means the components of the
crystal vectors, q(icar, np) is the coordinates of the qpoints and
nr(ipol) are the dimensions
of the FFT grid formed by the q-point grid. What I don't understand is
why the three parameters multiply and sum for x, y and z
components:that is,
          do icar=1,3
              xq = xq + at(icar,ipol) * q(icar,nq) * nr(ipol)
           end do
and then there is another line: lq = lq .and. (abs(nint(xq) - xq) .lt. eps
what makes (abs(nint(xq) - xq) should be less than eps.
Is there anyone familiar with this part? Any small suggestions may be
a great help for me.
Thanks for your help!
Best wishes,
Guoying

From giannozz at nest.sns.it  Wed Dec  5 09:50:46 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 5 Dec 2007 09:50:46 +0100
Subject: [Pw_forum] CRASH when running example18
In-Reply-To: <770551.44077.qm@web43143.mail.sp1.yahoo.com>
References: <770551.44077.qm@web43143.mail.sp1.yahoo.com>
Message-ID: <D5F01D4C-3B91-4A12-9D9D-53CB80FDD65F@nest.sns.it>


On Dec 4, 2007, at 22:13 , Peiqing Shen wrote:

>      from cp_read_cell : error #         1
>      cannot open restart file for reading:
> /home/staff/pshen/tmp/cp_93.save/data-file.xml

> It's true that there is no file in the directory
> /home/staff/pshen/tmp/cp_93.save
>
> Could any one let me know what happened when restarting CP.X?

may I suggest that you try to find out what happened at the end of
the previous run instead?

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 njuxuyuehua at gmail.com  Wed Dec  5 14:57:37 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Wed, 5 Dec 2007 21:57:37 +0800
Subject: [Pw_forum] a superficial question about the same parameters in
	relax and scf
Message-ID: <aca2feb20712050557k2f1eacd2q5df63556a342df51@mail.gmail.com>

hi everyone :
i have a question about the main  parameters used in relax and scf ,for
example :ecutwfc   ,
  ecutrho  ,if  i have test them in relax ,and whether i should retest
them when i do scf ,or enlarge them ,because ,in other software ,if you want
to get more accurate energy ,you are asked to enlarge some
parameters similar to  ecutwfc  , ecutrho    etc.
maybe ,it is a foolish or misunderstanding  questions .but i hope you could
help me ,to understanding how and why .
tahnk you



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From egk at gatech.edu  Wed Dec  5 15:11:50 2007
From: egk at gatech.edu (EG Kim)
Date: Wed, 05 Dec 2007 09:11:50 -0500
Subject: [Pw_forum] diago_full_acc
Message-ID: <1196863910.4756b1a65b1ec@webmail.mail.gatech.edu>

Dear Forum Subscribers,

I am trying to calculate the DOS and band structure ('nscf' and 'bands') with
full accuracy for unoccupied states.  I tried "diago_full_acc" but the results
don't seem affected compared to those without the keyword.  A portion of my
input file is attached below (all calculations were done with v3.2.3).  Thanks
much for reading.

Regards,

EG Kim

###############################################################################
&control
  calculation = 'nscf'
  pseudo_dir = '....'
  prefix = '....'
/
&system
  ibrav = 8
  a = 7.9
  b = 28.0
  c = 6.8
  cosbc = 0.0
  cosac = 0.0
  cosab = 0.0
  nat = 140
  ntyp = 4
  ecutwfc = 25.0
  nbnd = 292
  occupations = 'tetrahedra'
/
&electrons
  conv_thr = 1.0D-6
  diago_full_acc = .true.
/
K_POINTS automatic
  6  2  8   0 0 0

ATOMIC_SPECIES
  C   12.0107   C.blyp-v.UPF
  S   32.0650   S.blyp-v.UPF
  O   15.9994   O.blyp-v.UPF
  H   1.00794   H.blyp-v.UPF

+ -
| E.-G. Kim, Ph.D.
| School of Chemistry and Biochemistry
| 901 Atlantic Drive NW
| Georgia Institute of Technology
| Atlanta, GA 30332-0001
| U.S.A.
+ -

From akohlmey at cmm.chem.upenn.edu  Wed Dec  5 15:29:06 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 5 Dec 2007 09:29:06 -0500 (EST)
Subject: [Pw_forum] a superficial question about the same parameters in
 relax and scf
In-Reply-To: <aca2feb20712050557k2f1eacd2q5df63556a342df51@mail.gmail.com>
References: <aca2feb20712050557k2f1eacd2q5df63556a342df51@mail.gmail.com>
Message-ID: <Pine.LNX.4.64.0712050919400.2217@localhost.localdomain>

On Wed, 5 Dec 2007, xu yuehua wrote:

hi!

please respect the policy of this forum to add an
affiliation and then pick up a text book about quantum
chemistry and read about the variational principle.

the basis set size (in plane waves) is determined by
ecutwfc. the higher the cutoff, the larger the basis set
the lower the energy. we are essentially all doing calculations
with an incomplete basis set, but as long as the error
is small enough, it does not matter. it is you job to
find out what is enough and that can be different for
each calculation.

ecutrho is usually coupled to ecutwfc and determines the
real space representation of the density (which enters
the evaluation of the density functional(s)). for norm-
conserving pseudopotentials, this has a ration of 1:4
and there is little reason to change it. for ultra-soft
pseudopotentials, additional contribution to the density
(e.g. augmentation charges) have to be added to the 
real space density and for that you may need a higher
density cutoff. as ratio of 1:10 is frequently used when
high accuracy is wanted, but in some cases it may need
to be higher.

you didn't mention k-point sampling. depending on the
size and nature of your system, this is another dimension
of parameters that need to be converged to get accurate
results. please take the time and search through the
mailing list archives on these topics. there were many
discussions and each system and problem has its own 
quirks and needs adjustments (or not). 

hope this helps,

   axel.

XY> hi everyone :
XY> i have a question about the main  parameters used in relax and scf ,for
XY> example :ecutwfc   ,
XY>   ecutrho  ,if  i have test them in relax ,and whether i should retest
XY> them when i do scf ,or enlarge them ,because ,in other software ,if you want
XY> to get more accurate energy ,you are asked to enlarge some
XY> parameters similar to  ecutwfc  , ecutrho    etc.
XY> maybe ,it is a foolish or misunderstanding  questions .but i hope you could
XY> help me ,to understanding how and why .
XY> tahnk you
XY> 
XY> 
XY> 
XY> 

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

From paulatto at sissa.it  Wed Dec  5 15:42:09 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Wed, 5 Dec 2007 15:42:09 +0100 (CET)
Subject: [Pw_forum] diago_full_acc
In-Reply-To: <1196863910.4756b1a65b1ec@webmail.mail.gatech.edu>
References: <1196863910.4756b1a65b1ec@webmail.mail.gatech.edu>
Message-ID: <21772.147.122.5.182.1196865729.squirrel@webmail.sissa.it>


On Wed, December 5, 2007 15:11, EG Kim wrote:
>   conv_thr = 1.0D-6
>   diago_full_acc = .true.


Dear Kim,
the recipe used to determine the diagonalization accuracy is a bit
complicated; I think that in your specific case setting the diago_full_acc
uses almost the same threshold as the default case.

As you are doing a nscf calculation setting diago_thr_init to a small
value (1.e-10 is probably more than enough) should do the trick. If you
don't do that the default value is used (conv_thr/nelec for filled bands,
1.e-5 for empty ones.

bye


-- 
Lorenzo Paulatto
+39 040 3787 511
http://people.sissa.it/~paulatto/


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From giannozz at nest.sns.it  Wed Dec  5 16:09:22 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 5 Dec 2007 16:09:22 +0100
Subject: [Pw_forum] Help
In-Reply-To: <47562770.7080608@gmail.com>
References: <47562770.7080608@gmail.com>
Message-ID: <CA260B79-6614-43EE-83A8-D6345B4A29ED@nest.sns.it>


On Dec 5, 2007, at 5:22 , John K. Dogbe wrote:

> Could anyone kindly help me understand the following errors I got  
> during
> "make all" on SGI Origin 200?  I'm using SGI compiler and I have
> compiled fftw2.1.5 for use. Could there be a problem with my fftw  
> build?

no, it is completely unrelated, the problem is in the compilation of the
iotk toolkit.

>  use iotk_attr_interf
>                                  ^
> f90-1108 mfef90: ERROR IOTK_COPY_DAT_AUX_X, File = iotk_misc.F90,  
> Line = 341, Column = 34
>   The type of the actual argument, "Cray character pointer", does  
> not match "CHARACTER", the type of the dummy argument.

there are no "Cray character pointers" in the code. Old versions of  
the SGI
compiler are unable to compile any serious (and even not-so-serious)
fortran-90. I am afraid you need a newer version of the compiler.

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 marcel at physik.tu-berlin.de  Wed Dec  5 18:51:35 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Wed, 5 Dec 2007 18:51:35 +0100 (CET)
Subject: [Pw_forum] Plot phonon dispersion
In-Reply-To: <20071119151946.V44136@rosa.physik-pool.tu-berlin.de>
References: <20071119151946.V44136@rosa.physik-pool.tu-berlin.de>
Message-ID: <20071205184124.R26286@rosa.physik-pool.tu-berlin.de>

Dear list members,

i have written a small python /script-program to convert the matdyn output 
matdyn.freq into a two-column format that I want to share with you.
This can easily be plotted by xmgrace, gnuplot etc.

For simplicity I took the absolute value of the k-vector, so one has to 
modify the 1st column for non-cubic systems.

Best
Marcel


I just see, my email program is wrapping lines, so below has to be 
modified, the attachment works.



------> program starts here

# small program to convert freq-Output into two-column dat
# written by Marcel Mohr
# usage: python mat2agr.py freqfile > phonons.dat
# Caution:# in the output, the absolute value of k-vector is taken -> 1,1,1 
#->sqrt(3)
#
import sys,string
import os
import math
import re

#
def flatten(lst):
         for elem in lst:
                 if type(elem) in (tuple, list):
                         for i in flatten(elem):
                                 yield i
                 else:
                         yield elem

atom=[]
steps= 0
kk=0
input = open(sys.argv[1],'r')
line=input.readline()
#print line
bla=line.split()
if bla==[]:
         pass
elif bla[1]=="nbnd=":
# komma muss weg
         bla[2]=re.compile( "," ).sub( '', bla[2] )
         nbnd=string.atoi(bla[2])
#       print nbnd
         nkpt=string.atoi(bla[4])
#       print nkpt

# Anzahl der Lines sind jetzt nktp + nkpt *(nbnd/6)
lines=input.readlines()
for n, bla in enumerate(lines):
         dummy=0
# bloedes \n am Ende weg
for i in range(n+1):
         lines[i]=re.compile( "\n" ).sub( '' , lines[i] )
# Wir haben jetzt die Anzahl der Linien, Jetzt die Anzahl pro k-punkt 
#(nprok)
# 6 pro Spalte (also nbnd/6), falls nicht durch 6 teilbar, muss man plus 1 
#zahlen
if (nbnd%6)==0:
         nprok=nbnd/6
else:
         nprok=nbnd/6 + 1

kabslist=[]
freqlist=[]
for j in range(nkpt):
         klist=[]
         #linnum: only lines in which k-point info is stored
         linnum=j*(nprok+1)
         kptstr=lines[linnum].split()
         klist=[]
         for i in range(3):
                 k=string.atof(kptstr[i])
                 klist.append(k)
         kabslist.append( math.sqrt( klist[0]**2 + klist[1]**2 + 
klist[2]**2 ))
         freqK=[]
         for i in range(nprok):
                 freqK.append( lines[linnum+1+i].split())
         dummy=list(flatten(freqK))
         freqlist.append(dummy)

#output
for i in range(nbnd):
         for j in range(nkpt):
                 print ("%9.9f    %9.9f") %(kabslist[j],string.atof( 
freqlist[j][i]) )
         print " "
         print " "
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From degironc at sissa.it  Wed Dec  5 21:43:45 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 05 Dec 2007 21:43:45 +0100
Subject: [Pw_forum] about Fermi Energy shift in periodic (q=0)
	perturbations
In-Reply-To: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>
References: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>
Message-ID: <47570D81.70305@sissa.it>

dear Ezad Shojaee,
At any q/=0 the perturbation is such that the number of electrons does 
not change.
Even in the limit of q->0 the macroscopic term in the density response 
is zero (because in a metal
the dielectic constant is infinite).
Now consider the case of a periodic (q=0) perturbation, the simplest 
one, a constant, threated with or w/o the FE shift... which of the two 
treatments corresponds to the result you would obtain in the liimit  q->0 ?

please provide your affiliation

Stefano de Gironcoli - SISSA and DEMOCRITOS



Ezad Shojaee wrote:
> Hi
> can anyone refer me to some speciefic references about how and 
> why perodic perturbations(q=0) shift Fermi Energy in metals(in detail)?
> Thanx 
>
> ------------------------------------------------------------------------
> Explore the seven wonders of the world Learn more! 
> <http://search.msn.com/results.aspx?q=7+wonders+world&mkt=en-US&form=QBRE> 
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From degironc at sissa.it  Wed Dec  5 21:51:56 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 05 Dec 2007 21:51:56 +0100
Subject: [Pw_forum] question on q2r.f90
In-Reply-To: <6234c0c60712042305u51ef13cbmfef8bd7df7be1a3b@mail.gmail.com>
References: <6234c0c60712042305u51ef13cbmfef8bd7df7be1a3b@mail.gmail.com>
Message-ID: <47570F6C.5060307@sissa.it>

in q2r one declares a regular grid and then provide a number of matrices 
that should correspond to that grid.
This is what is checked in that part of the code.
If this is the error you get, some of your q-points does not correspond 
to the grid you declared.

Stefano de Gironcoli - SISSA and DEMOCRITOS

PS: Please provide your affiliation

Guoying Gao wrote:
> Dear everyone,
>       When I read the routine q2r.f90 given in the pwtools directory,
> I find the following lines:
>   %%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>         lq = .true.
>         do ipol=1,3
>            xq = 0.0
>            do icar=1,3
>               xq = xq + at(icar,ipol) * q(icar,nq) * nr(ipol)
>            end do
>            lq = lq .and. (abs(nint(xq) - xq) .lt. eps)
>            iq = nint(xq)
>            !
>            m(ipol)= mod(iq,nr(ipol)) + 1
>            if (m(ipol) .lt. 1) m(ipol) = m(ipol) + nr(ipol)
>         end do
>         if (.not.lq) call errore('init','q not allowed',1)
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> I know the parameters at(icar, ipol) means the components of the
> crystal vectors, q(icar, np) is the coordinates of the qpoints and
> nr(ipol) are the dimensions
> of the FFT grid formed by the q-point grid. What I don't understand is
> why the three parameters multiply and sum for x, y and z
> components:that is,
>           do icar=1,3
>               xq = xq + at(icar,ipol) * q(icar,nq) * nr(ipol)
>            end do
> and then there is another line: lq = lq .and. (abs(nint(xq) - xq) .lt. eps
> what makes (abs(nint(xq) - xq) should be less than eps.
> Is there anyone familiar with this part? Any small suggestions may be
> a great help for me.
> Thanks for your help!
> Best wishes,
> Guoying
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From gaoguoying at gmail.com  Thu Dec  6 03:30:11 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Thu, 6 Dec 2007 10:30:11 +0800
Subject: [Pw_forum] question on q2r.f90
In-Reply-To: <47570F6C.5060307@sissa.it>
References: <6234c0c60712042305u51ef13cbmfef8bd7df7be1a3b@mail.gmail.com>
	<47570F6C.5060307@sissa.it>
Message-ID: <6234c0c60712051830p20fed7y93d3b8db0be9ad32@mail.gmail.com>

Dear Stefano,
   Thanks for your reply.
> If this is the error you get, some of your q-points does not correspond
> to the grid you declared.
I searched the answers to the question on "q not allowed" in the
archive and got the following suggestions:
(1) generate q-points via PW/kpoint_grid.f90 substitute pwtools/kpoints.f
(2) use>3.0 version
I have generated q-points via PW/kpoint_grid.f90 and I'm testing it
using 3.2 version.
If I have got the succesful results, I will tell you as soon possible.
All the best,
Guoying,

From oulihui666 at 126.com  Thu Dec  6 10:08:23 2007
From: oulihui666 at 126.com (oulihui666)
Date: Thu, 6 Dec 2007 17:08:23 +0800 (CST)
Subject: [Pw_forum] About nelec and tot_charge
Message-ID: <19114153.801701196932103607.JavaMail.coremail@bj126app75.126.com>

Dear pwscf users,   I want to do a structural relaxation of a charged system using pwscf. For example, In the process of oxygen reduction reaction, adsorption of hydration proton(H3O+) on Pt(111) surface,  simultaneously, a extra electron is added, that is to say, O2 + H+ + e- . When I calculate this system with pwscf, could I add charge and add a electron simultanously?  I will be glad to learn some extra tricks related to fast scf convergence in such scenarios.       Thanks in advance      Lihui Ou   
--
======================================Lihui OuPH.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 akohlmey at cmm.chem.upenn.edu  Thu Dec  6 14:51:20 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Thu, 6 Dec 2007 08:51:20 -0500 (EST)
Subject: [Pw_forum] About nelec and tot_charge
In-Reply-To: <19114153.801701196932103607.JavaMail.coremail@bj126app75.126.com>
References: <19114153.801701196932103607.JavaMail.coremail@bj126app75.126.com>
Message-ID: <Pine.LNX.4.64.0712060846300.11020@localhost.localdomain>

On Thu, 6 Dec 2007, oulihui666 wrote:

dear lihui ou,

LO> Dear pwscf users, I want to do a structural relaxation of a charged 
LO> system using pwscf. For example, In the process of oxygen reduction 
LO> reaction, adsorption of hydration proton(H3O+) on Pt(111) surface, 
LO> simultaneously, a extra electron is added, that is to say, O2 + H+ + 
LO> e- . When I calculate this system with pwscf, could I add charge and 
LO> add a electron simultanously?  I will be glad to learn some extra 

there is no difference between changing the total charge and
adding an electron. those two parameters in the input are 
connected and you'll get an error message if they are not
consistent. 

LO> tricks related to fast scf convergence in such scenarios.  Thanks in 

charged systems, particularly with excess electrons 
can indeed be tricky to converge. there are a lot of
hints in the quantum espresso website and in the mailing
list archive. which of those may apply or not to your
system is difficult to predict. getting fast convergence
is a bit of a craft based on empirical knowledge, i.e.
there is no alternative to practicing and experimenting
to learn the "tricks of the trade".

cheers,
   axel.

LO> advance Lihui Ou


LO> --
LO> ======================================Lihui OuPH.D Candidate in Electrochemistry                     College of Chemistry and Molecular Science           Wuhan University,430072,Hubei Province,China E-mail:oulihui666 at 126.com======================================

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

From vietbacchemist at gmail.com  Fri Dec  7 04:06:47 2007
From: vietbacchemist at gmail.com (Viet Bac)
Date: Fri, 7 Dec 2007 12:06:47 +0900
Subject: [Pw_forum] Problem with q2r.x running
In-Reply-To: <ea64856c0712032012hf72ef8elf1f785bc46063880@mail.gmail.com>
References: <ea64856c0712032012hf72ef8elf1f785bc46063880@mail.gmail.com>
Message-ID: <ea64856c0712061906w4aca717emdf13741f0c6eddd1@mail.gmail.com>

Dear Dr. Paolo,

Thank you for your answer,
I found that when I decrease the threshold for SC in el-ph calculation
tr2_ph =1e-14, q2r.x cannot read a2Fq2r data.
It works with tr2_ph =1e-10. So could you please help me to solve this
problem from q2r.f90?

Bac

------------------------------
Phung Viet Bac
Division of Mathematical and Physical Science,
Graduate School of Natural Science and Technology,
Kanazawa University,
Kakuma, Kanazawa 920-1192, JAPAN




> (Is there any problem with a2Fq2r.* data??)

sure there is one, and it is explicitle stated in
the error message:

> forrtl: severe (59): list-directed I/O syntax error, unit 51,
> file /../a2Fq2r.51


Paolo
---
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 gaoguoying at gmail.com  Fri Dec  7 05:25:25 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Fri, 7 Dec 2007 12:25:25 +0800
Subject: [Pw_forum] question on q2r.f90
In-Reply-To: <6234c0c60712051830p20fed7y93d3b8db0be9ad32@mail.gmail.com>
References: <6234c0c60712042305u51ef13cbmfef8bd7df7be1a3b@mail.gmail.com>
	<47570F6C.5060307@sissa.it>
	<6234c0c60712051830p20fed7y93d3b8db0be9ad32@mail.gmail.com>
Message-ID: <6234c0c60712062025n46a02912g1125d28b05e7b9dc@mail.gmail.com>

Dear Stefano,
    I have got the successful results, the error of "q not allowed"
does not happen this time.
Thanks for your help!
Good luck!
Guoying

From gaoguoying at gmail.com  Fri Dec  7 05:41:44 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Fri, 7 Dec 2007 12:41:44 +0800
Subject: [Pw_forum] question on matdyn.x
Message-ID: <6234c0c60712062041rd0b002dm581cc30b27a90348@mail.gmail.com>

Dear everyone,
     When I do the calculation of phonon density of states using the
quantum-espresso-3.2 code, it gives the following errors:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
    PGFIO-F-239/namelist read/unit=5/entity name is not member of group.
   File name = stdin     formatted, sequential access   record = 8
   In source file matdyn.F90, at line number 195
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

The input parameters for DOS are listed as follows:
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
&input
    asr='simple',
    dos=.true.,
    amass(1)=1.00794,
    amass(2)=72.61,
    flfrc='ab.fc',
    nk1=2,nk2=2,nk3=2,
    deltaE=1.0,
    fldos='ab.dos'
 /
EOF
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Before we calculate DOS we have got the ab.fc file. We have tried
different nk1,nk2,nk3, but the errors
still happen. Does anyone know the reason for this? Any suggestions
will be apprecialted.
Thanks in advance.
Guoying
National Lab of Superhard Materials, JiLin University, P.R.China

From eyvaz_isaev at yahoo.com  Fri Dec  7 10:44:26 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 7 Dec 2007 01:44:26 -0800 (PST)
Subject: [Pw_forum] question on matdyn.x
In-Reply-To: <6234c0c60712062041rd0b002dm581cc30b27a90348@mail.gmail.com>
Message-ID: <223773.82010.qm@web60320.mail.yahoo.com>

Hi,

The problem is connected to your mistake in the input
file.
For electronic DOS calculations you use DeltaE, but
for phonon DOS calcuations one shoud use ndos=NNNN
instead of DeltaE.
So, it is not affected by nk1,nk2,nk3 set, of course.

Bests,
Eyvaz.

--- Guoying Gao <gaoguoying at gmail.com> wrote:

> Dear everyone,
>      When I do the calculation of phonon density of
> states using the
> quantum-espresso-3.2 code, it gives the following
> errors:
> 
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>     PGFIO-F-239/namelist read/unit=5/entity name is
> not member of group.
>    File name = stdin     formatted, sequential
> access   record = 8
>    In source file matdyn.F90, at line number 195
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> The input parameters for DOS are listed as follows:
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> &input
>     asr='simple',
>     dos=.true.,
>     amass(1)=1.00794,
>     amass(2)=72.61,
>     flfrc='ab.fc',
>     nk1=2,nk2=2,nk3=2,
>     deltaE=1.0,
>     fldos='ab.dos'
>  /
> EOF
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> Before we calculate DOS we have got the ab.fc file.
> We have tried
> different nk1,nk2,nk3, but the errors
> still happen. Does anyone know the reason for this?
> Any suggestions
> will be apprecialted.
> Thanks in advance.
> Guoying
> National Lab of Superhard Materials, JiLin
> University, P.R.China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From gaoguoying at gmail.com  Fri Dec  7 12:03:12 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Fri, 7 Dec 2007 19:03:12 +0800
Subject: [Pw_forum] question on matdyn.x
In-Reply-To: <223773.82010.qm@web60320.mail.yahoo.com>
References: <6234c0c60712062041rd0b002dm581cc30b27a90348@mail.gmail.com>
	<223773.82010.qm@web60320.mail.yahoo.com>
Message-ID: <6234c0c60712070303n1107a221r516f92d23dd7c933@mail.gmail.com>

Dear Eyvaz,
         I have got the successful results following your suggestions.
Thanks for your kindly help.
Guoying

From gaoguoying at gmail.com  Fri Dec  7 12:43:05 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Fri, 7 Dec 2007 19:43:05 +0800
Subject: [Pw_forum] question on q2r.f90
In-Reply-To: <6234c0c60712062025n46a02912g1125d28b05e7b9dc@mail.gmail.com>
References: <6234c0c60712042305u51ef13cbmfef8bd7df7be1a3b@mail.gmail.com>
	<47570F6C.5060307@sissa.it>
	<6234c0c60712051830p20fed7y93d3b8db0be9ad32@mail.gmail.com>
	<6234c0c60712062025n46a02912g1125d28b05e7b9dc@mail.gmail.com>
Message-ID: <6234c0c60712070343t3a4c4727n25acd8aa750ea85f@mail.gmail.com>

Dear everyone,
    In the last but one email, there are some mistakes in my expression.
   >>I have generated q-points via PW/kpoint_grid.f90 and I'm testing it
   >>using 3.2 version.
       I just used 3.2 version, it generates qpoints automatically
through ph.x, not via PW/kpoint_grid.f90.
   I'm sorry for misleading you.
Good luck!
Guoying

From gaoguoying at gmail.com  Fri Dec  7 16:13:09 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Fri, 7 Dec 2007 23:13:09 +0800
Subject: [Pw_forum] question on ibrav=0
Message-ID: <6234c0c60712070713k7fa1407al875e287738fd9ac@mail.gmail.com>

Dear everyone,
    I read the manual of QE and find that for ibrav=0, the
CELL_PARAMETERS has two choices.
one is cubic and the other is hexagonal. So I want to know in which
case we use cubic and  in which
one the other.
Thanks for you reply!
Guoying
National Lab of Superhard Materials, JiLin Univ. P.R.China

From paulatto at sissa.it  Fri Dec  7 16:26:19 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Fri, 7 Dec 2007 16:26:19 +0100 (CET)
Subject: [Pw_forum] question on ibrav=0
In-Reply-To: <6234c0c60712070713k7fa1407al875e287738fd9ac@mail.gmail.com>
References: <6234c0c60712070713k7fa1407al875e287738fd9ac@mail.gmail.com>
Message-ID: <6975.147.122.5.182.1197041179.squirrel@webmail.sissa.it>


On Fri, December 7, 2007 16:13, Guoying Gao wrote:
> Dear everyone,
>     I read the manual of QE and find that for ibrav=0, the
> CELL_PARAMETERS has two choices.
> one is cubic and the other is hexagonal. So I want to know in which
> case we use cubic and  in which
> one the other.

Dear Guoying Gao,
I'm just copying and pasting from Doc/INPUT_PW, but I think this is what
you wanted to know:

CELL_PARAMETERS

  optional card, needed only if ibrav = 0 is specified, ignored otherwise

  Syntax:

    CELL_PARAMETERS { cubic | hexagonal }
      a(1,1) a(2,1) a(3,1)
      a(1,2) a(2,2) a(3,2)
      a(1,3) a(2,3) a(3,3)

  a(:,1) = crystal axis 1    alat units   if celldm(1) was specified
      2                 2    a.u.         if celldm(1)=0
      3                 3
  Keyword "cubic" or "hexagonal" specify if you want to look for symmetries
  derived from the cubic symmetry group (default) or from the hexagonal
  symmetry group (assuming c axis as the z axis, a axis along the x axis)


-- 
Lorenzo Paulatto
+39 040 3787 511
http://people.sissa.it/~paulatto/


----------------------------------------------------------------
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From gaoguoying at gmail.com  Sun Dec  9 11:24:26 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Sun, 9 Dec 2007 18:24:26 +0800
Subject: [Pw_forum] question on ibrav=0
In-Reply-To: <6975.147.122.5.182.1197041179.squirrel@webmail.sissa.it>
References: <6234c0c60712070713k7fa1407al875e287738fd9ac@mail.gmail.com>
	<6975.147.122.5.182.1197041179.squirrel@webmail.sissa.it>
Message-ID: <6234c0c60712090224g6c2a9735md46715a9a821d6c1@mail.gmail.com>

Hi Lorenzo,
   I got it. Thanks for your helpful reply!
Guoying

From gaoguoying at gmail.com  Sun Dec  9 12:17:11 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Sun, 9 Dec 2007 19:17:11 +0800
Subject: [Pw_forum] calculating lambda for a phonon band structure with
	imaginary frequencies
Message-ID: <6234c0c60712090317h5095b067udcec235d0990b17d@mail.gmail.com>

Dear everyone,
      I intend to do the electron-phonon coupling calculation.
However, I found some  imaginary frequencies in the phonon band
structure.
So is it reasonable to calculate the lambda for the qpoints with
imaginary frequencies and why?
Thanks very much!
Guoying
National Lab of Superhard Materials, JiLin Univ, P. R. China

From baroni at sissa.it  Sun Dec  9 14:06:47 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 9 Dec 2007 13:06:47 +0000
Subject: [Pw_forum] calculating lambda for a phonon band structure with
	imaginary frequencies
In-Reply-To: <6234c0c60712090317h5095b067udcec235d0990b17d@mail.gmail.com>
References: <6234c0c60712090317h5095b067udcec235d0990b17d@mail.gmail.com>
Message-ID: <0D139674-C1FF-44EE-B12A-2132E8AC49EA@sissa.it>

Imaginary frequencies are usually a sign of a mechanical instability,  
as discussed many times in this forum as well as in many condensed- 
matter textbooks. I think the answer is yours: if you want to  
calculate the electron-phonon interaction of an instable (possibly  
metastable) phase of a material, please do. If instead instability is  
soemething that troubles you, then you better settle your troubles  
first. Cheers - SB

On Dec 9, 2007, at 11:17 AM, Guoying Gao wrote:

> Dear everyone,
>      I intend to do the electron-phonon coupling calculation.
> However, I found some  imaginary frequencies in the phonon band
> structure.
> So is it reasonable to calculate the lambda for the qpoints with
> imaginary frequencies and why?
> Thanks very much!
> Guoying
> National Lab of Superhard Materials, JiLin Univ, P. R. China
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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



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From gaoguoying at gmail.com  Sun Dec  9 15:27:41 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Sun, 9 Dec 2007 22:27:41 +0800
Subject: [Pw_forum] calculating lambda for a phonon band structure with
	imaginary frequencies
In-Reply-To: <0D139674-C1FF-44EE-B12A-2132E8AC49EA@sissa.it>
References: <6234c0c60712090317h5095b067udcec235d0990b17d@mail.gmail.com>
	<0D139674-C1FF-44EE-B12A-2132E8AC49EA@sissa.it>
Message-ID: <6234c0c60712090627o798334b6h8cf312c51b7a283d@mail.gmail.com>

On Dec 9, 2007 9:06 PM, Stefano Baroni <baroni at sissa.it> wrote:
> Imaginary frequencies are usually a sign of a mechanical instability, as
> discussed many times in this forum as well as in many condensed-matter
> textbooks. I think the answer is yours: if you want to calculate the
> electron-phonon interaction of an instable (possibly metastable) phase of a
> material, please do. If instead instability is soemething that troubles you,
> then you better settle your troubles first. Cheers - SB
Hi Stefano,
     Thanks for your reply.
     I know the imaginary frequencies signifying a mechanical
instability, but I want to know whether we can calculate it or not and
is it meanful to do this? We just want to estimate the values of Tc.
Guoying

From meisam_a84 at yahoo.com  Sun Dec  9 16:31:57 2007
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Sun, 9 Dec 2007 07:31:57 -0800 (PST)
Subject: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub
Message-ID: <832336.80553.qm@web30605.mail.mud.yahoo.com>

Dear all
during optimizing the a lattice in a zigzag nanotube there was a problem , the run for celldm(1) is done but for the upper cell dimensions it stops and the error is : wrong atomic cordinates. of cours in the output file of the former is written : davidson diagnolization with overlap . I don't know if it makes problem.
input:
&CONTROL
                 calculation = 'scf' ,
                restart_mode = 'restart' ,
                      outdir = '/home/meisam/projhe/5-0/band/scratch/' ,
                  pseudo_dir = '/home/meisam/espresso-3.1.1/pseudo/' ,
                      prefix = 'cnt18-scf' ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 18,
                   celldm(3) = 0.447232826,
                         nat = 25,
                        ntyp = 1,
                     ecutwfc = 30 ,
 /
 &ELECTRONS
 /
ATOMIC_SPECIES
    C   12.00000  C.pz-vbc.UPF
ATOMIC_POSITIONS angstrom
    C      1.958200000    0.000000000   -1.420000000
    C      0.605100000    1.862300000   -1.420000000
    C     -1.584200000    1.151000000   -1.420000000                                                   
    C     -1.584200000   -1.151000000   -1.420000000
    C      0.605100000   -1.862300000   -1.420000000
    C      1.584200000    1.151000000   -0.710000000
    C     -0.605100000    1.862300000   -0.710000000
    C     -1.958200000    0.000000000   -0.710000000
    C     -0.605100000   -1.862300000   -0.710000000
    C      1.584200000   -1.151000000   -0.710000000
    C      1.584200000    1.151000000    0.710000000
    C     -0.605100000    1.862300000    0.710000000
    C     -1.958200000    0.000000000    0.710000000
    C     -0.605100000   -1.862300000    0.710000000
    C      1.584200000   -1.151000000    0.710000000
    C      1.958200000    0.000000000    1.420000000
    C      0.605100000    1.862300000    1.420000000
    C     -1.584200000    1.151000000    1.420000000
    C     -1.584200000   -1.151000000    1.420000000
    C      0.605100000   -1.862300000    1.420000000
    C      1.958200000    0.000000000    2.840000000
    C      0.605100000    1.862300000    2.840000000
    C     -1.584200000    1.151000000    2.840000000
    C     -1.584200000   -1.151000000    2.840000000
    C      0.605100000   -1.862300000    2.840000000
K_POINTS automatic
  1 1 14   1 1 1


      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
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From hande at newton.physics.metu.edu.tr  Sun Dec  9 16:43:45 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Sun, 9 Dec 2007 17:43:45 +0200 (EET)
Subject: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub
In-Reply-To: <832336.80553.qm@web30605.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.44.0712091735280.14176-100000@newton.physics.metu.edu.tr>

Dear Meisam,

Your cell is still not periodic and there is still overlap between your
atoms. I believe it would be OK if you just chopped off the atoms forming
the leftmost ring of your nanotube. This would amount to just getting rid
of the last five atoms while keeping everything the same. Please invest
some time in visualizing your structure with xcrysden and paying attention
to its error messages.

Best of luck, 
Hande

On Sun, 9 Dec 2007, meisam aghtar wrote:

> Dear all
> during optimizing the a lattice in a zigzag nanotube there was a problem , the run for celldm(1) is done but for the upper cell dimensions it stops and the error is : wrong atomic cordinates. of cours in the output file of the former is written : davidson diagnolization with overlap . I don't know if it makes problem.
> input:
> &CONTROL
>                  calculation = 'scf' ,
>                 restart_mode = 'restart' ,
>                       outdir = '/home/meisam/projhe/5-0/band/scratch/' ,
>                   pseudo_dir = '/home/meisam/espresso-3.1.1/pseudo/' ,
>                       prefix = 'cnt18-scf' ,
>  /
>  &SYSTEM
>                        ibrav = 4,
>                    celldm(1) = 18,
>                    celldm(3) = 0.447232826,
>                          nat = 25,
>                         ntyp = 1,
>                      ecutwfc = 30 ,
>  /
>  &ELECTRONS
>  /
> ATOMIC_SPECIES
>     C   12.00000  C.pz-vbc.UPF
> ATOMIC_POSITIONS angstrom
>     C      1.958200000    0.000000000   -1.420000000
>     C      0.605100000    1.862300000   -1.420000000
>     C     -1.584200000    1.151000000   -1.420000000                                                   
>     C     -1.584200000   -1.151000000   -1.420000000
>     C      0.605100000   -1.862300000   -1.420000000
>     C      1.584200000    1.151000000   -0.710000000
>     C     -0.605100000    1.862300000   -0.710000000
>     C     -1.958200000    0.000000000   -0.710000000
>     C     -0.605100000   -1.862300000   -0.710000000
>     C      1.584200000   -1.151000000   -0.710000000
>     C      1.584200000    1.151000000    0.710000000
>     C     -0.605100000    1.862300000    0.710000000
>     C     -1.958200000    0.000000000    0.710000000
>     C     -0.605100000   -1.862300000    0.710000000
>     C      1.584200000   -1.151000000    0.710000000
>     C      1.958200000    0.000000000    1.420000000
>     C      0.605100000    1.862300000    1.420000000
>     C     -1.584200000    1.151000000    1.420000000
>     C     -1.584200000   -1.151000000    1.420000000
>     C      0.605100000   -1.862300000    1.420000000
>     C      1.958200000    0.000000000    2.840000000
>     C      0.605100000    1.862300000    2.840000000
>     C     -1.584200000    1.151000000    2.840000000
>     C     -1.584200000   -1.151000000    2.840000000
>     C      0.605100000   -1.862300000    2.840000000
> K_POINTS automatic
>   1 1 14   1 1 1
> 
> 
>       ____________________________________________________________________________________
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> 

-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande


From konstantin_kudin at yahoo.com  Sun Dec  9 17:13:52 2007
From: konstantin_kudin at yahoo.com (Konstantin Kudin)
Date: Sun, 9 Dec 2007 08:13:52 -0800 (PST)
Subject: [Pw_forum] phonon with nspin=2 - not implemented ?
Message-ID: <726707.91701.qm@web57706.mail.re3.yahoo.com>

 All,

 I ran the following PW/PH calculation for an insulating system:
PW input:
nspin=2
multiplicity=1
starting_magnetization(1)=0.15
starting_magnetization(2)=-0.15

 Then, the PH code crashed with the message:

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from phq_readin : error #         1
     The phonon code with constrained magnetization is not yet
available

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

 Compared to other options already in PH, the one with nspin=2 for
insulators seems rather less demanding. Is there any big reason why it
is not implemented? Or, can one use some kind of a workaround here?

 Thanks!
 Kostya


      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 


From baroni at sissa.it  Sun Dec  9 19:41:03 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Sun, 9 Dec 2007 18:41:03 +0000
Subject: [Pw_forum] calculating lambda for a phonon band structure with
	imaginary frequencies
In-Reply-To: <6234c0c60712090627o798334b6h8cf312c51b7a283d@mail.gmail.com>
References: <6234c0c60712090317h5095b067udcec235d0990b17d@mail.gmail.com>
	<0D139674-C1FF-44EE-B12A-2132E8AC49EA@sissa.it>
	<6234c0c60712090627o798334b6h8cf312c51b7a283d@mail.gmail.com>
Message-ID: <47411777-E7B4-41EB-BECF-C6A6F7F1957D@sissa.it>


On Dec 9, 2007, at 2:27 PM, Guoying Gao wrote:

> On Dec 9, 2007 9:06 PM, Stefano Baroni <baroni at sissa.it> wrote:
>> Imaginary frequencies are usually a sign of a mechanical  
>> instability, as
>> discussed many times in this forum as well as in many condensed- 
>> matter
>> textbooks. I think the answer is yours: if you want to calculate the
>> electron-phonon interaction of an instable (possibly metastable)  
>> phase of a
>> material, please do. If instead instability is soemething that  
>> troubles you,
>> then you better settle your troubles first. Cheers - SB
> Hi Stefano,
>     Thanks for your reply.
>     I know the imaginary frequencies signifying a mechanical
> instability, but I want to know whether we can calculate it or not and
> is it meanful to do this?

as said, I think that only you can be the judge
S.

> We just want to estimate the values of Tc.
> Guoying
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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



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From akohlmey at cmm.chem.upenn.edu  Sun Dec  9 19:58:55 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Sun, 9 Dec 2007 13:58:55 -0500 (EST)
Subject: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub
In-Reply-To: <832336.80553.qm@web30605.mail.mud.yahoo.com>
References: <832336.80553.qm@web30605.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.64.0712091348570.11020@localhost.localdomain>

On Sun, 9 Dec 2007, meisam aghtar wrote:

MA> Dear all

dear meisam,

MA> during optimizing the a lattice in a zigzag nanotube there was a 
MA> problem , the run for celldm(1) is done but for the upper cell 
MA> dimensions it stops and the error is : wrong atomic cordinates. of 

this usually means, that atom positions do overlap.
did you check for this?


MA> cours in the output file of the former is written : davidson 
MA> diagnolization with overlap . I don't know if it makes problem.

no.

what is odd, that you write you want to optimize the lattice,
but you specify _absolute_ coordinates (in angstrom). this way
only the box dimensions change, not that (relative) atom positions.
when people usually say, they want to optimize the lattice, they
mean, that they want to find the optimal lattice parameter and 
then they use relative positions (alat or crystal units). absolute
coordinates make sense, when you want to "optimize" the vacuum
around a cluster. with a nanotube system, though, you have both.

please check, whether your input makes sense (-> xcrysden)
and then try to explain a bit more clearly what you want to
do, if you still have problems.

cheers,
    axel.

p.s.: are you sure a 30ry plane wave energy cutoff is sufficient
for the type of pseudopotential (norm-conserving) you are using?
no point in trying to optimize lattice parameter when your basis
set is incomplete...

MA> input:
MA> &CONTROL
MA>                  calculation = 'scf' ,
MA>                 restart_mode = 'restart' ,
MA>                       outdir = '/home/meisam/projhe/5-0/band/scratch/' ,
MA>                   pseudo_dir = '/home/meisam/espresso-3.1.1/pseudo/' ,
MA>                       prefix = 'cnt18-scf' ,
MA>  /
MA>  &SYSTEM
MA>                        ibrav = 4,
MA>                    celldm(1) = 18,
MA>                    celldm(3) = 0.447232826,
MA>                          nat = 25,
MA>                         ntyp = 1,
MA>                      ecutwfc = 30 ,
MA>  /
MA>  &ELECTRONS
MA>  /
MA> ATOMIC_SPECIES
MA>     C   12.00000  C.pz-vbc.UPF
MA> ATOMIC_POSITIONS angstrom
MA>     C      1.958200000    0.000000000   -1.420000000

[...]


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

From giannozz at nest.sns.it  Sun Dec  9 22:16:05 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Sun, 9 Dec 2007 22:16:05 +0100
Subject: [Pw_forum] phonon with nspin=2 - not implemented ?
In-Reply-To: <726707.91701.qm@web57706.mail.re3.yahoo.com>
References: <726707.91701.qm@web57706.mail.re3.yahoo.com>
Message-ID: <0A3CD717-6C5D-495E-869F-3ABC2C1BC2F0@nest.sns.it>

On Dec 9, 2007, at 17:13 , Konstantin Kudin wrote:

> I ran the following PW/PH calculation for an insulating system:
>  [...]
> nspin=2
> multiplicity=1
> [...]
>  Then, the PH code crashed with the message:
> [...]
>      The phonon code with constrained magnetization is not yet  
> available
> [...]
>  Compared to other options already in PH, the one with nspin=2 for
> insulators seems rather less demanding. Is there any big reason why it
> is not implemented?

nothing big, but, as usual, there is a reason for such behavior.
"multiplicity=1" forces the system to have a definite magnetization
state. This is done by setting two Fermi energies, one for spin-up
and one for spin-down. This information is written in the data file
and if the phonon code notices it, it stops for the reason mentioned
in the error message.

> Or, can one use some kind of a workaround here?


If the magnetization you chose is the ground-state one, the two Fermi  
energies
will be the same (or they will be equivalent in the case of  
insulators). In that
case, commenting out the check in phq_readin.f90 should work. If you  
constrain
the magnetization to a value that is not the ground state, I have no  
idea what
numbers will come out

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 nest.sns.it  Sun Dec  9 22:17:29 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Sun, 9 Dec 2007 22:17:29 +0100
Subject: [Pw_forum] Problem with q2r.x running
In-Reply-To: <ea64856c0712061906w4aca717emdf13741f0c6eddd1@mail.gmail.com>
References: <ea64856c0712032012hf72ef8elf1f785bc46063880@mail.gmail.com>
	<ea64856c0712061906w4aca717emdf13741f0c6eddd1@mail.gmail.com>
Message-ID: <1047A0DB-F0C5-443B-9128-3D551D27E9FA@nest.sns.it>


On Dec 7, 2007, at 4:06 , Viet Bac wrote:

> Dear Dr. Paolo [...]
> I found that when I decrease the threshold for SC in el-ph  
> calculation tr2_ph =1e-14,
> q2r.x cannot read a2Fq2r data. It works with tr2_ph =1e-10. So  
> could you please help
> me to solve this problem from q2r.f90?

no I cannot. You can: look what is different between the two cases

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 jibiaoli at gmail.com  Mon Dec 10 11:52:12 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Mon, 10 Dec 2007 18:52:12 +0800
Subject: [Pw_forum] Local density of electronic entropy
Message-ID: <b8b82da20712100252xc2e938aka6829ce95a9c44d3@mail.gmail.com>

Dear PWscf users,
I am very appreciated getting some literature or theoretical background
about 'local density of electronic entropy'. Thanks again!

-- 
Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23925323
Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
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From meisam_a84 at yahoo.com  Mon Dec 10 12:00:41 2007
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Mon, 10 Dec 2007 03:00:41 -0800 (PST)
Subject: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub
Message-ID: <861856.45640.qm@web30602.mail.mud.yahoo.com>

Dear all 
thank hande for your answer.
the pw run for celldm(1)=17 is done of course with this message: davidson diagnolization with overlap in the output. but for the upper celldms the run stops. 
there is no overlap in xcrysden visualization.


----- Original Message ----
From: Hande Ustunel <hande at newton.physics.metu.edu.tr>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Sunday, December 9, 2007 7:13:45 PM
Subject: Re: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub

Dear Meisam,

Your cell is still not periodic and there is still overlap between your
atoms. I believe it would be OK if you just chopped off the atoms forming
the leftmost ring of your nanotube. This would amount to just getting rid
of the last five atoms while keeping everything the same. Please invest
some time in visualizing your structure with xcrysden and paying attention
to its error messages.

Best of luck, 
Hande

On Sun, 9 Dec 2007, meisam aghtar wrote:

> Dear all
> during optimizing the a lattice in a zigzag nanotube there was a problem , the run for celldm(1) is done but for the upper cell dimensions it stops and the error is : wrong atomic cordinates. of cours in the output file of the former is written : davidson diagnolization with overlap . I don't know if it makes problem.
> input:
> &CONTROL
>                  calculation = 'scf' ,
>                restart_mode = 'restart' ,
>                      outdir = '/home/meisam/projhe/5-0/band/scratch/' ,
>                  pseudo_dir = '/home/meisam/espresso-3.1.1/pseudo/' ,
>                      prefix = 'cnt18-scf' ,
>  /
>  &SYSTEM
>                        ibrav = 4,
>                    celldm(1) = 18,
>                    celldm(3) = 0.447232826,
>                          nat = 25,
>                        ntyp = 1,
>                      ecutwfc = 30 ,
>  /
>  &ELECTRONS
>  /
> ATOMIC_SPECIES
>    C  12.00000  C.pz-vbc.UPF
> ATOMIC_POSITIONS angstrom
>    C      1.958200000    0.000000000  -1.420000000
>    C      0.605100000    1.862300000  -1.420000000
>    C    -1.584200000    1.151000000  -1.420000000                                                  
>    C    -1.584200000  -1.151000000  -1.420000000
>    C      0.605100000  -1.862300000  -1.420000000
>    C      1.584200000    1.151000000  -0.710000000
>    C    -0.605100000    1.862300000  -0.710000000
>    C    -1.958200000    0.000000000  -0.710000000
>    C    -0.605100000  -1.862300000  -0.710000000
>    C      1.584200000  -1.151000000  -0.710000000
>    C      1.584200000    1.151000000    0.710000000
>    C    -0.605100000    1.862300000    0.710000000
>    C    -1.958200000    0.000000000    0.710000000
>    C    -0.605100000  -1.862300000    0.710000000
>    C      1.584200000  -1.151000000    0.710000000
>    C      1.958200000    0.000000000    1.420000000
>    C      0.605100000    1.862300000    1.420000000
>    C    -1.584200000    1.151000000    1.420000000
>    C    -1.584200000  -1.151000000    1.420000000
>    C      0.605100000  -1.862300000    1.420000000
>    C      1.958200000    0.000000000    2.840000000
>    C      0.605100000    1.862300000    2.840000000
>    C    -1.584200000    1.151000000    2.840000000
>    C    -1.584200000  -1.151000000    2.840000000
>    C      0.605100000  -1.862300000    2.840000000
> K_POINTS automatic
>  1 1 14  1 1 1
> 
> 
>      ____________________________________________________________________________________
> Be a better friend, newshound, and 
> know-it-all with Yahoo! Mobile.  Try it now.   http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 
> 

-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande

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From giannozz at nest.sns.it  Mon Dec 10 12:20:34 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 10 Dec 2007 12:20:34 +0100
Subject: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub
In-Reply-To: <861856.45640.qm@web30602.mail.mud.yahoo.com>
References: <861856.45640.qm@web30602.mail.mud.yahoo.com>
Message-ID: <6853159B-A947-4C29-A09E-C06773AE1955@nest.sns.it>


On Dec 10, 2007, at 12:00 , meisam aghtar wrote:

> the pw run for celldm(1)=17 is done of course with this message:
> davidson diagnolization with overlap in the output.
> but for the upper celldms the run stops.
> there is no overlap in xcrysden visualization.

the "overlap" in davidson diagonalization has nothing to do with
"overlapping" atomic coordinates. If the code says "wrong
atomic coordinates", your atomic coordinates are wrong,
i.e., too close.

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 hande at newton.physics.metu.edu.tr  Mon Dec 10 12:50:06 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Mon, 10 Dec 2007 13:50:06 +0200 (EET)
Subject: [Pw_forum] erro wrong attomic cordinates for 5-0 nanotub
In-Reply-To: <6853159B-A947-4C29-A09E-C06773AE1955@nest.sns.it>
Message-ID: <Pine.LNX.4.44.0712101347060.22672-100000@newton.physics.metu.edu.tr>

Dear Meisam, 

Believe me there is overlap in the file in the input you have provided.

Please try these atomic coordinates :

 C   1.958200000  0.000000000 -1.420000000
 C   0.605100000  1.862300000 -1.420000000
 C  -1.584200000  1.151000000 -1.420000000
 C  -1.584200000 -1.151000000 -1.420000000
 C   0.605100000 -1.862300000 -1.420000000
 C   1.584200000  1.151000000 -0.710000000
 C  -0.605100000  1.862300000 -0.710000000
 C  -1.958200000  0.000000000 -0.710000000
 C  -0.605100000 -1.862300000 -0.710000000
 C   1.584200000 -1.151000000 -0.710000000
 C   1.584200000  1.151000000  0.710000000
 C  -0.605100000  1.862300000  0.710000000
 C  -1.958200000  0.000000000  0.710000000
 C  -0.605100000 -1.862300000  0.710000000
 C   1.584200000 -1.151000000  0.710000000
 C   1.958200000  0.000000000  1.420000000
 C   0.605100000  1.862300000  1.420000000
 C  -1.584200000  1.151000000  1.420000000
 C  -1.584200000 -1.151000000  1.420000000
 C   0.605100000 -1.862300000  1.420000000

changing of course nat to 20. I've tried your input with this change and it
works just fine. There are of course other issues such as the possible
inadequacy of the ecut for your norm-conserving pseudo and your choice of
angstrom to specify the coordinates as pointed out by other people.

Best,
Hande

On Mon, 10 Dec 2007, Paolo Giannozzi wrote:

> 
> On Dec 10, 2007, at 12:00 , meisam aghtar wrote:
> 
> > the pw run for celldm(1)=17 is done of course with this message:
> > davidson diagnolization with overlap in the output.
> > but for the upper celldms the run stops.
> > there is no overlap in xcrysden visualization.
> 
> the "overlap" in davidson diagonalization has nothing to do with
> "overlapping" atomic coordinates. If the code says "wrong
> atomic coordinates", your atomic coordinates are wrong,
> i.e., too close.
> 
> 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
> 

-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande



From zhs064 at mail.usask.ca  Mon Dec 10 20:20:05 2007
From: zhs064 at mail.usask.ca (zhs064)
Date: Mon, 10 Dec 2007 13:20:05 -0600
Subject: [Pw_forum] how to convert a pseudopotential with semi-core states
 generated by OPIUM to PWSCF UPF format?
Message-ID: <475D9165.2050500@mail.usask.ca>

hi, all
      I'm a novice of PWscf. Does anybody know how to convert a
pseudopotential with semi-core states generated by OPIUM to PWscf
UPF format? Are there some programs for that or some suggestions.
     Thank you very much!

Victor
zhs064 at usask.mail.ca

From paulatto at sissa.it  Mon Dec 10 22:06:12 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 10 Dec 2007 22:06:12 +0100 (CET)
Subject: [Pw_forum] how to convert a pseudopotential with semi-core
 states generated by OPIUM to PWSCF UPF format?
In-Reply-To: <475D9165.2050500@mail.usask.ca>
References: <475D9165.2050500@mail.usask.ca>
Message-ID: <26582.80.183.42.220.1197320772.squirrel@webmail.sissa.it>


On Mon, December 10, 2007 20:20, zhs064 wrote:
> hi, all
>       I'm a novice of PWscf. Does anybody know how to convert a
> pseudopotential with semi-core states generated by OPIUM to PWscf
> UPF format? Are there some programs for that or some suggestions.
>      Thank you very much!

Dear Victor,
once I did it, so it is possible. You should use one of the ___2upf tools
that you can find in the upftools subdirectory, I don't remeber wich one
but it should be possible to guess it from the file extension.

To build the upf tools you have to "make upf".

I hope this helps, Lorenzo.

P.s. please sign your posts with full name and surname, and affiliation if
possible.

-- 
Lorenzo Paulatto
+39 040 3787 511
http://people.sissa.it/~paulatto/


----------------------------------------------------------------
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From giannozz at nest.sns.it  Mon Dec 10 22:47:35 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 10 Dec 2007 22:47:35 +0100
Subject: [Pw_forum] how to convert a pseudopotential with semi-core
	states generated by OPIUM to PWSCF UPF format?
In-Reply-To: <26582.80.183.42.220.1197320772.squirrel@webmail.sissa.it>
References: <475D9165.2050500@mail.usask.ca>
	<26582.80.183.42.220.1197320772.squirrel@webmail.sissa.it>
Message-ID: <522DA46A-3133-45DB-BAB4-3468C52873FF@nest.sns.it>


On Dec 10, 2007, at 22:06 , Lorenzo Paulatto wrote:

>> Does anybody know how to convert a pseudopotential with semi-core
>> states generated by OPIUM to PWscf UPF format? Are there some
>> programs for that or some suggestions.

> once I did it, so it is possible. You should use one of the ___2upf  
> tools
> that you can find in the upftools subdirectory, I don't remember  
> wich one
> but it should be possible to guess it from the file extension.

If I remember correctly, OPIUM can directly generate PPs in the old
PWscf "ncpp" format. It may be converted into UPF but it is not (yet)
necessary: PWscf still supports the old formats

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 Jeremie.Teyssier at physics.unige.ch  Tue Dec 11 08:39:44 2007
From: Jeremie.Teyssier at physics.unige.ch (=?iso-8859-1?Q?J=E9r=E9mie_Teyssier?=)
Date: Tue, 11 Dec 2007 08:39:44 +0100
Subject: [Pw_forum] use of Virtual.x
Message-ID: <013d01c83bc8$ffc6dd60$6401a8c0@PORTABLE>

To people doing virtual crystal approximation

 

These last weeks, I tried to figure out whether the modified version of
virtual.x was leading to reasonable pseudopotentials for VCA.

Modified means simply that I removed the error message


I have build 2 mixable pseudopotentials; same functional, same rinners, same
number nature of wavefunctions and projectors.

Then I mixed it uo using Virtual.x

Apparently it works. You get an output pseudopotential with reasonable shape
but there are many things wrong.

-          I compared the results of calculation with that potential with
super-cell calculation with the same original potentials and the result if
not completely different reveals a huge overestimate of the exchange
splitting (I am calculating magnetic structures.)  in the case of VCA.

-          More worrying, I mixed Co and Mn pseudopotentials in a 50/50
ratio and the results (again mainly the magnetisation) is completely
different (40%) between 0.5xCo+0.5xMn and 0.5xMn+0.5xCo


-          Another trouble when I mixed Co and Mn with 100% of one of the
two compounds. Then a mix of 100% Of Co (or Mn) is not equivalent to pure Co
(or Mn) pseudo.

I would say with my small experience that virtual.x is on the way to work
but if you use it, do some simple tests before even if you thing that the
resulting potential looks correct. Surprisingly, I got reasonable results
mixing Fe and Co pseudo from pwscf library.

As a conclusion and I am now trying to compare the two ways, for people
doing VCA, I suggest building a new pseudopotential directly from Vanderbild
code. Then, even if you get weird results, you have an access to all
parameter of the pseudo generation


If people have another experience on VCA with pwscf, please contact me.

 

J?r?mie

 

Jeremie Teyssier

DPMC

24 quai Ernest Ensermet

CH-1211 Geneve 4

SUISSE

tel: (41) 22 379 35 68

fax: (41) 22 379 68 69

web:  <http://optics.unige.ch/jeremie/home_jeremie.html>
http://optics.unige.ch/jeremie/home_jeremie.html

 

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From oulihui666 at 126.com  Tue Dec 11 11:55:17 2007
From: oulihui666 at 126.com (oulihui666)
Date: Tue, 11 Dec 2007 18:55:17 +0800 (CST)
Subject: [Pw_forum] A problem about plotrho
Message-ID: <13171357.2745201197370517891.JavaMail.coremail@bj126app75.126.com>

Dear pwscf users,
   I have a question, quite naive. I tried to search the charge density of oxygen molecular, but I have to rely on your advice. as well as I know,the calculation procedes as follows:
1) make a self-consistent calculation (input=O2.scf.in)
2) run the postprocessing program pp.x (input=O2.pp_rho.in)
3) run plotrho.x program (input=O2.plotrho.in, output=O2.plotrho.out)in order to produce a postscript file: O2.rho.ps.
   According to the calculation procedes, I try to calculate the charge density of oxygen molecular. the program plotrho was used as follows:
(1)scf calculation:
 &CONTROL
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/olh/tmp/' ,
                  pseudo_dir = '/home/olh/pseudo/' ,
                      prefix = 'O2' ,
                     tstress = .true. ,
                     tprnfor = .true. ,
 /
 &SYSTEM
                       ibrav = 1,
                   celldm(1) = 15.117815,
                         nat = 2,
                        ntyp = 1,
                     ecutwfc = 30 ,
                     ecutrho = 300 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'gaussian' ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.5,
 /
 &ELECTRONS
                    conv_thr = 1.D-6 ,
                 mixing_beta = 0.4D0 ,
             diagonalization = 'david' ,
 /
ATOMIC_SPECIES
    O   15.99900  O.pbe-rrkjus.UPF 
ATOMIC_POSITIONS angstrom 
    O      0.000000000    0.000000000    0.416410572    0  0  0 
    O      0.000000000    0.000000000    1.653589428    0  0  0 
K_POINTS automatic 
  4 4 1   1 1 1 
(2)postprocessing program pp.x
 &INPUTPP
                      prefix = 'O2' ,
                      outdir = '/home/olh/tmp/' ,
                     filplot = 'O2-charge' ,
                    plot_num = 0,
 /
 &PLOT
                       nfile = 1 ,
                   filepp(1) = 'O2-charge',
                   weight(1) = 1.0,
                     fileout = 'O2.rho.dat' ,
                       iflag = 2 ,
               output_format = 2 ,
                       e1(1) = 1,
                       e1(2) = 0,
                       e1(3) = 0,
                       e2(1) = 0,
                       e2(2) = 1,
                       e2(3) = 0,
                       x0(1) = 0,
                       x0(2) = 0,
                       x0(3) = 0,
                          nx = 56 ,
                          ny = 40 ,
 /
(3)plotrho.x program
    O2.rho.dat
    O2.rho.ps
    n
    0 0.09 6
However, when I calculated (3), in order to produce a postscript file: O2.rho.ps, I encounter a problem, it displayed as follows:

"PGFIO-F-225/list-directed read/unit=5/lexical error--unknown token type.
File name = stdin    Formatted, sequential access  record = 3
In source file plotrho.F90, at line number 129."
Any suggestions is appreciated.
 
Thank you in advance
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 fratesi at mater.unimib.it  Tue Dec 11 12:30:53 2007
From: fratesi at mater.unimib.it (Guido Fratesi)
Date: Tue, 11 Dec 2007 12:30:53 +0100 (CET)
Subject: [Pw_forum] A problem about plotrho
In-Reply-To: <13171357.2745201197370517891.JavaMail.coremail@bj126app75.126.com>
References: <13171357.2745201197370517891.JavaMail.coremail@bj126app75.126.com>
Message-ID: <Pine.LNX.4.64.0712111227190.30474@localhost>

Dear Lihui Ou,

maybe you already considered this, but running plotrho.x interactively may 
help. Indeed, the detailed input of such program depends on a few 
conditions, for example if there's negative charge you will not be asked 
whether to use logarithmic scale.
Hope this helps.
Guido

On Tue, 11 Dec 2007, oulihui666 wrote:

> Dear pwscf users,
>   I have a question, quite naive. I tried to search the charge density of oxygen molecular, but I have to rely on your advice. as well as I know,the calculation procedes as follows:
> 1) make a self-consistent calculation (input=O2.scf.in)
> 2) run the postprocessing program pp.x (input=O2.pp_rho.in)
> 3) run plotrho.x program (input=O2.plotrho.in, output=O2.plotrho.out)in order to produce a postscript file: O2.rho.ps.
[...]
> (3)plotrho.x program
>    O2.rho.dat
>    O2.rho.ps
>    n
>    0 0.09 6
> However, when I calculated (3), in order to produce a postscript file: O2.rho.ps, I encounter a problem, it displayed as follows:
>
> "PGFIO-F-225/list-directed read/unit=5/lexical error--unknown token type.
> File name = stdin    Formatted, sequential access  record = 3
> In source file plotrho.F90, at line number 129."
> Any suggestions is appreciated.
>
> Thank you in advance
> Lihui Ou

-- 
Guido Fratesi

Dipartimento di Scienza dei Materiali
Universita` degli Studi di Milano-Bicocca

From giannozz at nest.sns.it  Tue Dec 11 12:39:55 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 11 Dec 2007 12:39:55 +0100
Subject: [Pw_forum] A problem about plotrho
In-Reply-To: <13171357.2745201197370517891.JavaMail.coremail@bj126app75.126.com>
References: <13171357.2745201197370517891.JavaMail.coremail@bj126app75.126.com>
Message-ID: <EECC31DF-4730-4777-9170-4B8600CAD655@nest.sns.it>


On Dec 11, 2007, at 11:55 , oulihui666 wrote:

>                      tstress = .true.

calculating stress for a molecule is rather useless

> plotrho.x program

to be run interactively, prompts questions, waits for
(correct) answers...

> "PGFIO-F-225/list-directed read/unit=5/lexical error--unknown token  
> type.
> File name = stdin    Formatted, sequential access  record = 3
> In source file plotrho.F90, at line number 129."

...your answer was not correct

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 nest.sns.it  Tue Dec 11 12:40:06 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 11 Dec 2007 12:40:06 +0100
Subject: [Pw_forum] use of Virtual.x
In-Reply-To: <013d01c83bc8$ffc6dd60$6401a8c0@PORTABLE>
References: <013d01c83bc8$ffc6dd60$6401a8c0@PORTABLE>
Message-ID: <78F3F6BB-3C33-4A9E-BEF2-2089463454B7@nest.sns.it>


On Dec 11, 2007, at 8:39 , J?r?mie Teyssier wrote:

> Apparently it works [...]
> Another trouble when I mixed Co and Mn with 100% of one of the two  
> compounds.
> Then a mix of 100% Of Co (or Mn) is not equivalent to pure Co (or  
> Mn) pseudo.

so it doesn't work, by definition

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 nest.sns.it  Tue Dec 11 22:42:55 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Tue, 11 Dec 2007 22:42:55 +0100
Subject: [Pw_forum] Local density of electronic entropy
In-Reply-To: <b8b82da20712100252xc2e938aka6829ce95a9c44d3@mail.gmail.com>
References: <b8b82da20712100252xc2e938aka6829ce95a9c44d3@mail.gmail.com>
Message-ID: <0D28E239-B6EF-4814-9892-A612822DEB2D@nest.sns.it>


On Dec 10, 2007, at 11:52 , Clark Lee wrote:

> I am very appreciated getting some literature or theoretical  
> background
> about 'local density of electronic entropy'.

I am not aware of any specific reference and don't know what the
code that calculates it actually does; my guess is that it is the  
entropy
of a Fermi-Dirac gas, f log(f) + (1-f)log(1-f), where f is the occupancy
(can be found in textbooks), weighted with the local density of states
at the Fermi energy: \sum_i |\psi_i(r)|^2 \delta(E_F-e_i)

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 jhashemifar at gmail.com  Wed Dec 12 09:44:25 2007
From: jhashemifar at gmail.com (Javad hashemifar)
Date: Wed, 12 Dec 2007 12:14:25 +0330
Subject: [Pw_forum] how PAW should be used?
Message-ID: <2fb18d9f0712120044gada91fao96eb13bb69e02b6a@mail.gmail.com>

Dear PWscf developers and users

At the Isfahan University of Technology, it is couple of years that we are
using Quantum-Espresso for electronic structure calculations. So far mainly
we have used ultra soft pseudopotentials to calculate the electronic
structure of surfaces and interfaces.
Now we are interested to use a new feature of this code that is PAW
techniques but unfortunately the available documents and discussions on the
Forum, are not enough to find out the required procedure for using PAW
method. Hence it is highly appreciated if expert users learn us which
programs should be run for using PAW and which input files should be
adjusted .

Thank you in advance
S. Javad Hashemifar
Isfahan University of Technology

On Dec 10, 2007 2:22 PM, Clark Lee <jibiaoli at gmail.com> wrote:

> Dear PWscf users,
> I am very appreciated getting some literature or theoretical background
> about 'l ocal density of electronic entropy'. Thanks again!
>
> --
> Yours sincerely,
>
> Clark Lee
>
> State Key Lab of Corrosion and Protection (SKLCP)
> Institute of Metal Research (IMR)
> Chinese Academy of Sciences (CAS), China
> Phone: 024-23925323
> Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
======================================
Seyed Javad  Hashemifar,    Ph.D.
Tel:  +98-311-3912375       Fax: +98-311-3912376
Physics Department, Isfahan University of Technology
84156 Isfahan, Iran
---------------------------------------------------------------------------
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From degironc at sissa.it  Wed Dec 12 10:56:12 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 12 Dec 2007 10:56:12 +0100
Subject: [Pw_forum] how PAW should be used?
In-Reply-To: <2fb18d9f0712120044gada91fao96eb13bb69e02b6a@mail.gmail.com>
References: <2fb18d9f0712120044gada91fao96eb13bb69e02b6a@mail.gmail.com>
Message-ID: <475FB03C.3060705@sissa.it>

Dear Javad hashemifar and all,

the PAW method is currently under implementation in the PWscd code in 
the QE dsitribution (maily thanks to the work of Lorenzo Paulatto, a PhD 
SISSA student, and myself building upon important preliminary 
contributions from Guido Fratesi, a former PhD SISSA student, and 
Riccardo Mazzarello, a SISSA postdoc) .
It is nearly done and it will be described in the next release of QE 
(expected to come out some time next January).
 From the user point of view it should be very similar to an US 
peudopotential calculations.. one will simply need to provide a PAW 
dataset in the UPF format ....
Presently the extension of UPF format for PAW and a set of datasets for 
most  common elements is  under development...
It will takes some time to generate them and have same basic testing...
The contibution from the QE community to an extensive testing of these  
datasets will be  very much important  in the first few months from the 
release but we are not yet ready for that. now... though we are getting 
closer.

For the time being please be patient .

Useful literature for a description of the PAW method includes:
1) P.E.Bloechl, PRB 50, 17953 (1994),
2) N.A.W.Holzwart et al., PRB 55, 2005 (1997),
3) G.Kresse and D.Joubert, PRB 59, 1758 (1999).

Stefano de Gironcoli, SISSA and DEMOCRTITOS


Javad hashemifar wrote:
> Dear PWscf developers and users
>
> At the Isfahan University of Technology, it is couple of years that we 
> are using Quantum-Espresso for electronic structure calculations. So 
> far mainly we have used ultra soft pseudopotentials to calculate the 
> electronic structure of surfaces and interfaces.
> Now we are interested to use a new feature of this code that is PAW 
> techniques but unfortunately the available documents and discussions 
> on the Forum, are not enough to find out the required procedure for 
> using PAW method. Hence it is highly appreciated if expert users learn 
> us which programs should be run for using PAW and which input files 
> should be adjusted .
>
> Thank you in advance
> S. Javad Hashemifar
> Isfahan University of Technology
>
> On Dec 10, 2007 2:22 PM, Clark Lee <jibiaoli at gmail.com 
> <mailto:jibiaoli at gmail.com>> wrote:
>
>     Dear PWscf users,
>     I am very appreciated getting some literature or theoretical
>     background about 'l ocal density of electronic entropy'. Thanks again!
>
>     -- 
>     Yours sincerely,
>
>     Clark Lee
>
>     State Key Lab of Corrosion and Protection (SKLCP)
>     Institute of Metal Research (IMR)
>     Chinese Academy of Sciences (CAS), China
>     Phone: 024-23925323
>     Email: jibiaoli at imr.ac.cn <mailto:jibiaoli at imr.ac.cn> or
>     jibiaoli at gmail.com <mailto:jibiaoli at gmail.com>
>
>     _______________________________________________
>     Pw_forum mailing list
>     Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>     http://www.democritos.it/mailman/listinfo/pw_forum
>     <http://www.democritos.it/mailman/listinfo/pw_forum>
>
>
>
>
> -- 
> ======================================
> Seyed Javad  Hashemifar,    Ph.D.
> Tel:  +98-311-3912375       Fax: +98-311-3912376
> Physics Department, Isfahan University of Technology
> 84156 Isfahan, Iran
> --------------------------------------------------------------------------- 
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From vietbacchemist at gmail.com  Wed Dec 12 11:23:05 2007
From: vietbacchemist at gmail.com (Viet Bac)
Date: Wed, 12 Dec 2007 19:23:05 +0900
Subject: [Pw_forum] Strange phonon branches appear in phonon dispersion
Message-ID: <ea64856c0712120223r45b37246g2e8b3d02daac2afc@mail.gmail.com>

Dear Pw_users,

I am trying to do calculation phonon dispersion and EPC for 1D Aluminum
chain. I got the results which are strange phonon branches appearing. In the
case of 2 atom-cell, I got 4 phonon branches, two of them are Optical and
Acoustical phonon branches and two others, which have zero and negative
values, are unknown for me. In the case if I have 1 atom-cell, that strange
branch also appears. Could any body explain for me what kind of frequencies
here?

I was surfing this forum and FAQ and I found many discussion about negative
frequencies, but I still cannot find the answers for me.

Bac


This is my relaxed unitcell

For 1-atom cell

  input alat =      20.0000 (a.u.)

CELL_PARAMETERS (alat)
   0.999558675   0.000000000   0.000000000
   0.000000000   0.999558675   0.000000000
   0.000000000   0.000000000   0.224680571

ATOMIC_POSITIONS (angstrom)
Al       0.000000000   0.000000000   0.000000000

For 2-atom cell

CELL_PARAMETERS (alat)
   1.000000000   0.000000000   0.000000000
   0.000000000   1.000000000   0.000000000
   0.000000000   0.000000000   0.453300000

ATOMIC_POSITIONS (angstrom)
Al       0.000000000   0.000000000   2.399000000
Al       0.000000000   0.000000000   0.000000000

And INPUT for ph.x

 tr2_ph=1.0d-12,
  prefix='al_20',
  fildvscf='Al2v',
  amass(1)=26.98,
  outdir='/root/tmp/',
  fildyn='al2.dyn',
  elph=.true.,
  trans=.true.,
  ldisp=.true.
  nq1=1, nq2=1, nq3=10

------------------------------
Phung Viet Bac
Division of Mathematical and Physical Science,
Graduate School of Natural Science and Technology,
Kanazawa University,
Kakuma, Kanazawa 920-1192, JAPAN
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From degironc at sissa.it  Wed Dec 12 11:25:50 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 12 Dec 2007 11:25:50 +0100
Subject: [Pw_forum] Strange phonon branches appear in phonon dispersion
In-Reply-To: <ea64856c0712120223r45b37246g2e8b3d02daac2afc@mail.gmail.com>
References: <ea64856c0712120223r45b37246g2e8b3d02daac2afc@mail.gmail.com>
Message-ID: <475FB72E.6010307@sissa.it>

your phonon branches are really strange...
with two atoms I would expect 6 modes per each q-point

stefano

Viet Bac wrote:
> Dear Pw_users,
>
> I am trying to do calculation phonon dispersion and EPC for 1D 
> Aluminum chain. I got the results which are strange phonon branches 
> appearing. In the case of 2 atom-cell, I got 4 phonon branches, two of 
> them are Optical and Acoustical phonon branches and two others, which 
> have zero and negative values, are unknown for me. In the case if I 
> have 1 atom-cell, that strange branch also appears. Could any body 
> explain for me what kind of frequencies here?
>
> I was surfing this forum and FAQ and I found many discussion about 
> negative frequencies, but I still cannot find the answers for me.
>
> Bac
>


From marcel at physik.tu-berlin.de  Wed Dec 12 12:33:14 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Wed, 12 Dec 2007 12:33:14 +0100 (CET)
Subject: [Pw_forum] Strange phonon branches appear in phonon dispersion
In-Reply-To: <475FB72E.6010307@sissa.it>
References: <ea64856c0712120223r45b37246g2e8b3d02daac2afc@mail.gmail.com>
	<475FB72E.6010307@sissa.it>
Message-ID: <20071212121448.F52212@rosa.physik-pool.tu-berlin.de>

>> I am trying to do calculation phonon dispersion and EPC for 1D
>> Aluminum chain. I got the results which are strange phonon branches
>> appearing. In the case of 2 atom-cell, I got 4 phonon branches, two of
>> them are Optical and Acoustical phonon branches and two others, which
>> have zero and negative values, are unknown for me. In the case if I
>> have 1 atom-cell, that strange branch also appears. Could any body
>> explain for me what kind of frequencies here?

6 branches for 2 atom are what one expects (in general 3n branches and 3 
acoustical and 3n-3 optical ones).

However negative values indicate some error in your calculation, dependent 
on the magnitude and system.
You can impose some sum-rules for the acoustic ones, to force them to be 
0 at the Gamma point.

Acoustic forces are harder to calculate (smaller forces). In your case I 
would guess up to 15 cm^1 should be ok for the acoustic ones.
Negative optical ones should not occur.

Best
Marcel Mohr


>>
>> I was surfing this forum and FAQ and I found many discussion about
>> negative frequencies, but I still cannot find the answers for me.
>>
>> Bac
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


From njuxuyuehua at gmail.com  Wed Dec 12 13:02:56 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Wed, 12 Dec 2007 20:02:56 +0800
Subject: [Pw_forum] about the precision of energy and some extend problem.
Message-ID: <aca2feb20712120402y17f09de3jb5c3848ddc12af58@mail.gmail.com>

hi ,uesers here :
i relax one crystal lattice vs energy:
i have compute several energy list :

c          E(RY)
2.795  -137.79266
2.78   -137.79248
2.77   -137.79233
2.8     -137.7927
2.81  -137.79275
2.82  -137.79275
2.83  -137.79278
2.84  -137.79276
2.85  -137.79279
2.86  -137.79272
2.87  -137.79265
2.88  -137.79258
2.9   -137.79229
2.95  -137.79122
these energy points are smooth and  can be plotted  parabola.
the system has 12 atoms.the energy is different most at the third digit
after radix point. so i think the average energy/atom is less 0.0001.

i want to ask  the  within the precision of energy(my thinking is based on
that :my above calculation is set ecutwfc:29, ecutrho:200,and the  criterion
is 35,350, the convergence is 0.0049345 ry.)
so this small difference of energy can skip,i.e we can choose 2.77 which is
regarded as the best structure?
 as why i ask this question,for the the structure of 2.85 has two  big
negative frequencies  near -100cm-1, even if i add asr .
but 2.77 has no negative frequency after i add asr.


-- 
Xu Yuehua
physics Department of Nanjing university
China
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From hande at newton.physics.metu.edu.tr  Wed Dec 12 13:11:11 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Wed, 12 Dec 2007 14:11:11 +0200 (EET)
Subject: [Pw_forum] about the precision of energy and some extend
	problem.
In-Reply-To: <aca2feb20712120402y17f09de3jb5c3848ddc12af58@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0712121405530.23154-101000@newton.physics.metu.edu.tr>

Dear Xu Yuehua,

You should fit your energies to a parabola and find the minimum of the
fit. For a second order fit, your minimum is at about 2.83. 2.77 is just a
local blip in your rather jumpy data. You cannot decide by looking at the
individual energies because they do not follow a smooth function. But even
for the "wrong" lattice constant, there's no physical reason why you should
get negative frequencies if you have converged your electronic and atomic
coordinates to high accuracy. I'm attaching the fit as an example.

I would also suggest increasing your cutoff a little because your data, as
I said, is a bit noisy near the minimum.

Best,
Hande

On Wed, 12 Dec 2007, xu yuehua wrote:

> hi ,uesers here :
> i relax one crystal lattice vs energy:
> i have compute several energy list :
> 
> c          E(RY)
> 2.795  -137.79266
> 2.78   -137.79248
> 2.77   -137.79233
> 2.8     -137.7927
> 2.81  -137.79275
> 2.82  -137.79275
> 2.83  -137.79278
> 2.84  -137.79276
> 2.85  -137.79279
> 2.86  -137.79272
> 2.87  -137.79265
> 2.88  -137.79258
> 2.9   -137.79229
> 2.95  -137.79122
> these energy points are smooth and  can be plotted  parabola.
> the system has 12 atoms.the energy is different most at the third digit
> after radix point. so i think the average energy/atom is less 0.0001.
> 
> i want to ask  the  within the precision of energy(my thinking is based on
> that :my above calculation is set ecutwfc:29, ecutrho:200,and the  criterion
> is 35,350, the convergence is 0.0049345 ry.)
> so this small difference of energy can skip,i.e we can choose 2.77 which is
> regarded as the best structure?
>  as why i ask this question,for the the structure of 2.85 has two  big
> negative frequencies  near -100cm-1, even if i add asr .
> but 2.77 has no negative frequency after i add asr.
> 
> 
> 

-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande
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From dkorotin at gmail.com  Wed Dec 12 14:18:07 2007
From: dkorotin at gmail.com (Dmitry Korotin)
Date: Wed, 12 Dec 2007 18:18:07 +0500
Subject: [Pw_forum] Wave function to charge density
Message-ID: <2fd252650712120518q39811c4p1109ac219014f7d1@mail.gmail.com>

Dear ESPRESSO developers,
Could you explain me meaning and usage on nls(), nl() and igk()
arrays? Or, please answer on my concrete question:
I have some Wannier-function stored in array wf(1:npwx). The order of
plane waves in the array index is the same that used for evc() array.
Now I want to generate charge density of my Wannier-function in
G-space and add it to the total charge density in the cell (I can do
it in the routine electrons() before charge densities mixing).

It is clear that rho_{g,g'} = \sum_k wk*wf(g)*wf^{*}(g')
But how to convert this square array to linear array rhognew(ngm) form
used in the code (file electrons.f90)?

I know that my question is strongly technical, and, I think, not
interesting for other community members, but I have no other place to
ask.

Thank you in advance,
Dmitry Korotin
PhD student,
Institute of Metal Physics,
Ural branch of RAS,
Russia

From degironc at sissa.it  Wed Dec 12 14:52:11 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 12 Dec 2007 14:52:11 +0100
Subject: [Pw_forum] Wave function to charge density
In-Reply-To: <2fd252650712120518q39811c4p1109ac219014f7d1@mail.gmail.com>
References: <2fd252650712120518q39811c4p1109ac219014f7d1@mail.gmail.com>
Message-ID: <475FE78B.1080800@sissa.it>

the charge density is calculated in PW/sum_band.f90
the meaning of igk, nls, nl (that is the way they should be used in 
order to go from the indexing of evc to the fft grid)
is exemplified there.
hope this helps,
 stefano

Dmitry Korotin wrote:
> Dear ESPRESSO developers,
> Could you explain me meaning and usage on nls(), nl() and igk()
> arrays? Or, please answer on my concrete question:
> I have some Wannier-function stored in array wf(1:npwx). The order of
> plane waves in the array index is the same that used for evc() array.
> Now I want to generate charge density of my Wannier-function in
> G-space and add it to the total charge density in the cell (I can do
> it in the routine electrons() before charge densities mixing).
>
> It is clear that rho_{g,g'} = \sum_k wk*wf(g)*wf^{*}(g')
> But how to convert this square array to linear array rhognew(ngm) form
> used in the code (file electrons.f90)?
>   
> I know that my question is strongly technical, and, I think, not
> interesting for other community members, but I have no other place to
> ask.
>
> Thank you in advance,
> Dmitry Korotin
> PhD student,
> Institute of Metal Physics,
> Ural branch of RAS,
> Russia
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From efeomer76 at gmail.com  Wed Dec 12 18:29:48 2007
From: efeomer76 at gmail.com (=?ISO-8859-1?Q?=D6mer_Ko=E7?=)
Date: Wed, 12 Dec 2007 19:29:48 +0200
Subject: [Pw_forum] IFC's and eigendisplacements in example06
Message-ID: <75810c7f0712120929x72df3e4cuf8b60f66020c2273@mail.gmail.com>

Dear PWSCF users,

 My questions are about example06



1) Could you give me some analysis and explanations on the range of the
interatomic force constants (IFC's) for AlAs in example06.
 On the Forum, there are  some informations and explanations but i don't
understand them. I need more explanations.



alas444.fc



  2     2  2 10.5000000  0.0000000  0.0000000  0.0000000   0.0000000
0.0000000

           1   'Al '    24590.7655930491

           2   'As '    68285.4024548272

    1     1      0.0000000      0.0000000      0.0000000

    2     2      0.2500000      0.2500000      0.2500000

 T

     13.7439581       0.0000000      0.0000000

      0.0000000      13.7439581      0.0000000

      0.0000000       0.0000000     13.7439581

    1

      2.5582103       0.0000000      0.0000000

      0.0000000       2.5582103      0.0000000

      0.0000000       0.0000000      2.5582103

    2

     -2.5582103       0.0000000      0.0000000

      0.0000000      -2.5582103      0.0000000

      0.0000000       0.0000000     -2.5582103

   4    4   4

   1    1   1   1

   1    1   1   2.17004984418E-01

   2    1   1  -5.06952740903E-03

   3    1   1   9.99492789182E-05

   4    1   1  -5.06952740903E-03

   1    2   1   1.07967422105E-02

   2    2   1  -6.07584921925E-04

   3    2   1  -1.61474518909E-04

   4    2   1  -5.06952740903E-03

   1    3   1   4.18136269798E-03

   2    3   1  -6.07584921925E-04

   3    3   1   9.99492789182E-05

   4    3   1  -6.07584921925E-04

   1    4   1   1.07967422105E-02

   2    4   1  -5.06952740903E-03

   3    4   1  -1.61474518909E-04

   4    4   1  -6.07584921925E-04

   1    1   2  -5.06952740903E-03

   2    1   2  -1.61474518909E-04

   3    1   2  -6.07584921925E-04

   ????????????????????????????




2) Is there a meaning of ratio of displacement of the two ions (Al and As)
in the eigendisplacement pattern?
The calculated vibrational eigenvectors at X point are below. How can we
evaluate this data?



q =       0.0000       0.0000      1.0000

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

     omega( 1) =        2.841119 [THz] =      94.770143 [cm-1]

 (   0.611885   0.039292    -0.353070  -0.018348     0.000000    0.000000   )
Al

 ( -0.352406   -0.018313     0.610733   0.039218     0.000000   0.000000    )
As

     omega( 2) =        2.841119 [THz] =      94.770143 [cm-1]

 (   0.353530   0.003400     0.613143  -0.001588      0.000000   0.000000
)

 (   0.611989  -0.001585     0.352865   0.003394     0.000000    0.000000
)

     omega( 3) =        6.563802 [THz] =     218.946309 [cm-1]

 (   0.000000   0.000000     0.000000   0.000000     0.000000    0.000000
)

 (   0.000000   0.000000     0.000000   0.000000     1.000000    0.000000
)

     omega( 4) =       10.442067 [THz] =     348.312171 [cm-1]

 (   0.753056   0.016289    -0.563430   0.002731     0.000000    0.000000
)

 (   0.203284  -0.000985    -0.271700  -0.005877     0.000000    0.000000
)

     omega( 5) =       10.442067 [THz] =     348.312171 [cm-1]

 ( -0.563178   -0.017050    -0.753227  -0.002855     0.000000   0.000000
)

 (   0.271762   0.001030     0.203193   0.006152     0.000000    0.000000
)

     omega( 6) =       12.209736 [THz] =     407.275646 [cm-1]

 (   0.000000   0.000000     0.000000   0.000000    -0.138259    0.990396
)

 (   0.000000   0.000000     0.000000   0.000000     0.000000    0.000000
)

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

     diagonalizing the dynamical matrix ...


Many thanks in advance

?mer.


-- 
?mer Ko?
100. Y?l University
Dept of Physics Van, Turkey
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From jdogbe at gmail.com  Wed Dec 12 21:11:55 2007
From: jdogbe at gmail.com (John K. Dogbe)
Date: Wed, 12 Dec 2007 15:11:55 -0500
Subject: [Pw_forum] pools not implemented
Message-ID: <4760408B.5040208@gmail.com>

hi all!

I compiled qe v. 3.2.3 and decided to do something I usually don't do 
(sorry, I should have been doing it, depending on how one looks at it 
...).  I run the examples! In example01, I had a crash report on 
"cu.bands.in".  Here's the output:

Program POST-PROC v.3.2.3  starts ...
    Today is 12Dec2007 at 11: 9:52

    Parallel version (MPI)

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

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

    from bands : error #         2
    pools not implemented
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


    stopping ...

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

    from bands : error #         2
    pools not implemented
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


    stopping ...

 > My question is where's this coming from?  I noticed that this example 
is not in the previous release (3.1) and there are no problems with any 
of the examples I run from the earlier version. Other examples run 
smoothly. Hmmm ... just thought I should take out -npools passed to 
mpirun.  I will report the results soon.

Thanks,
John

-- 
============================================================
John K. Dogbe, Visiting Assistant Professor
Barton College, Dept. of Science & Mathematics
400 Atlantic Christian College Dr. NE, Wilson,NC 27893-2575
Tel.: (252) 399-6471, Fax.: (252) 399-6465        
============================================================
**The first is not necessarily the Leader**

        "If I have spoken evil, bear witness of the evil:
                but if well, why smitest thou me?"
                                -- Jesus Christ (John, 18:23)


From w2agz at pacbell.net  Wed Dec 12 21:32:44 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Wed, 12 Dec 2007 12:32:44 -0800
Subject: [Pw_forum] bands_FS.x and spin polarized metals
Message-ID: <000001c83cfe$26acd5c0$74068140$@net>

To All (especially Eyvaz Isaev!):

When I look at the source code for bands_FS, it seems unlikely that the
program will handle a spin-polarized metallic band structure (e.g., Ni.I
notice in Example 8, that its band structure is "unpolarized" before
applying bands_FS.x).  And sure enough, if you're dumb and try anyway, it
abends with a read error, probably because there's twice the number of
k-points out there that it expects.

If anyone out there wants to extend (or has extended) Eyvaz' code, I'd be a
willing alpha-tester.  

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


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From jdogbe at gmail.com  Wed Dec 12 21:40:06 2007
From: jdogbe at gmail.com (John K. Dogbe)
Date: Wed, 12 Dec 2007 15:40:06 -0500
Subject: [Pw_forum] pools not implemented - follow up
Message-ID: <47604726.6040608@gmail.com>

Hi,

Just following up on my previous question.  I did the run without 
-npools.  Turned out I did not get the CRASH file right away as was the 
previous case, but I did not wait for the runs (which happens for 
*.bands.in) because it was taking "awfully" long.  Can't afford to leave 
a test job running in my name on a borrowed computing resource.

Any ideas/suggestions will be appreciated.  I would need to utilize the 
bands calculations in actual run so, I can't ignore this. Please, see 
the original post below.
Thank you.
John



 > hi all!

I compiled qe v. 3.2.3 and decided to do something I usually don't do 
(sorry, I should have been doing it, depending on how one looks at it 
...).  I run the examples! In example01, I had a crash report on 
"cu.bands.in".  Here's the output:

Program POST-PROC v.3.2.3  starts ...
   Today is 12Dec2007 at 11: 9:52

   Parallel version (MPI)

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

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

   from bands : error #         2
   pools not implemented
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


   stopping ...

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 

   from bands : error #         2
   pools not implemented
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 


   stopping ...

 > My question is where's this coming from?  I noticed that this example 
is not in the previous release (3.1) and there are no problems with any 
of the examples I run from the earlier version. Other examples run 
smoothly. Hmmm ... just thought I should take out -npools passed to 
mpirun.  I will report the results soon.

Thanks,
John

-- 
============================================================
John K. Dogbe, Visiting Assistant Professor
Barton College, Dept. of Science & Mathematics
400 Atlantic Christian College Dr. NE, Wilson,NC 27893-2575
Tel.: (252) 399-6471, Fax.: (252) 399-6465        
============================================================
**The first is not necessarily the Leader**

        "If I have spoken evil, bear witness of the evil:
                but if well, why smitest thou me?"
                                -- Jesus Christ (John, 18:23)


From giannozz at nest.sns.it  Wed Dec 12 21:45:48 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 12 Dec 2007 21:45:48 +0100
Subject: [Pw_forum] pools not implemented
In-Reply-To: <4760408B.5040208@gmail.com>
References: <4760408B.5040208@gmail.com>
Message-ID: <BC13FE0D-8E45-4BA7-B3A6-79C63F03D193@nest.sns.it>


On Dec 12, 2007, at 21:11 , John K. Dogbe wrote:

>     from bands : error #         2
>     pools not implemented
>
>> My question is where's this coming from?

froms "bands", as the error message says. It is an
auxiliary program that makes plots of (guess what?)
the band structure. Pools, i.e. k-point parallelization,
is not implemented there because its implementation
wouldn't be completely straightforward. It might be an
exercise for somebody willing to learn parallel
programming, though.

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 nest.sns.it  Wed Dec 12 21:49:57 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 12 Dec 2007 21:49:57 +0100
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <000001c83cfe$26acd5c0$74068140$@net>
References: <000001c83cfe$26acd5c0$74068140$@net>
Message-ID: <11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it>


On Dec 12, 2007, at 21:32 , Paul M. Grant wrote:

> And sure enough, if you?re dumb and try anyway, it abends with a  
> read error
>

I am old enough to have seen card punchers in action, so the term
"abend" is not unknown to me, but I guess younger people don't
know that it is a shorthand for "abnormal end", on IBM mainframes...

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 eyvaz_isaev at yahoo.com  Wed Dec 12 21:50:14 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 12 Dec 2007 12:50:14 -0800 (PST)
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <000001c83cfe$26acd5c0$74068140$@net>
Message-ID: <263805.93742.qm@web60317.mail.yahoo.com>

Hi Paul,

Actually I have a version for spin-polarized bands,
and  can replace the code. Please wait just a few days
(to test it again), and we can plot spin-polarized FS.
 

Very bests,
Eyvaz. 

--- "Paul M. Grant" <w2agz at pacbell.net> wrote:

> To All (especially Eyvaz Isaev!):
> 
> When I look at the source code for bands_FS, it
> seems unlikely that the
> program will handle a spin-polarized metallic band
> structure (e.g., Ni.I
> notice in Example 8, that its band structure is
> "unpolarized" before
> applying bands_FS.x).  And sure enough, if you're
> dumb and try anyway, it
> abends with a read error, probably because there's
> twice the number of
> k-points out there that it expects.
> 
> If anyone out there wants to extend (or has
> extended) Eyvaz' code, I'd be a
> willing alpha-tester.  
> 
> Paul M. Grant, PhD
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford
> University
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com
>  
>  
> 
> 
> > _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping

From marzari at MIT.EDU  Wed Dec 12 21:58:46 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 12 Dec 2007 15:58:46 -0500
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it>
References: <000001c83cfe$26acd5c0$74068140$@net>
	<11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it>
Message-ID: <47604B86.8070207@mit.edu>

Paolo Giannozzi wrote:
> On Dec 12, 2007, at 21:32 , Paul M. Grant wrote:
> 
>> And sure enough, if you?re dumb and try anyway, it abends with a  
>> read error
>>
> 
> I am old enough to have seen card punchers in action, so the term
> "abend" is not unknown to me, but I guess younger people don't
> know that it is a shorthand for "abnormal end", on IBM mainframes...


What's a mainframe ? Is it like a really, really big ipod ?

				nicola


---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From giannozz at nest.sns.it  Wed Dec 12 22:12:15 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 12 Dec 2007 22:12:15 +0100
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <47604B86.8070207@mit.edu>
References: <000001c83cfe$26acd5c0$74068140$@net>
	<11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it>
	<47604B86.8070207@mit.edu>
Message-ID: <B5FACEDA-2DA5-4DD4-B3B2-0C1D243B7A6B@nest.sns.it>


On Dec 12, 2007, at 21:58 , Nicola Marzari wrote:

>> I am old enough to have seen card punchers in action, so the term
>> "abend" is not unknown to me, but I guess younger people don't
>> know that it is a shorthand for "abnormal end", on IBM mainframes...
>
> What's a mainframe ? Is it like a really, really big ipod ?

do you remember the picture of the "home computer
in 2004" you sent me some time ago ?
http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg
:-)

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 nest.sns.it  Wed Dec 12 22:15:47 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 12 Dec 2007 22:15:47 +0100
Subject: [Pw_forum] pools not implemented - follow up
In-Reply-To: <47604726.6040608@gmail.com>
References: <47604726.6040608@gmail.com>
Message-ID: <370A4B96-BAE1-49F9-86A6-5ED87FB30C2F@nest.sns.it>


On Dec 12, 2007, at 21:40 , John K. Dogbe wrote:

> I did not wait for the runs (which happens for *.bands.in) because
> it was taking "awfully" long.

example 01 alone should take no more than 2 minutes on a PC.
The complete suite will take a few hours.

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 eyvaz_isaev at yahoo.com  Wed Dec 12 22:52:12 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 12 Dec 2007 13:52:12 -0800 (PST)
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <B5FACEDA-2DA5-4DD4-B3B2-0C1D243B7A6B@nest.sns.it>
Message-ID: <531716.89372.qm@web60320.mail.yahoo.com>

Wow! So nice picture!
Well, if one can differentite it there will be lots of
i-Pods.

Bests,
Eyvaz.

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

> 
> On Dec 12, 2007, at 21:58 , Nicola Marzari wrote:
> 
> >> I am old enough to have seen card punchers in
> action, so the term
> >> "abend" is not unknown to me, but I guess younger
> people don't
> >> know that it is a shorthand for "abnormal end",
> on IBM mainframes...
> >
> > What's a mainframe ? Is it like a really, really
> big ipod ?
> 
> do you remember the picture of the "home computer
> in 2004" you sent me some time ago ?
>
http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg
> :-)
> 
> 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
> 


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


      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping

From eyvaz_isaev at yahoo.com  Wed Dec 12 23:53:44 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 12 Dec 2007 14:53:44 -0800 (PST)
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <000001c83cfe$26acd5c0$74068140$@net>
Message-ID: <108043.35715.qm@web60325.mail.yahoo.com>

Dear Paul,

I have just found the last version of the file. So,
let me to do some tests before sending it to you, and
the community.

Bests,
Eyvaz.

--- "Paul M. Grant" <w2agz at pacbell.net> wrote:

> To All (especially Eyvaz Isaev!):
> 
> When I look at the source code for bands_FS, it
> seems unlikely that the
> program will handle a spin-polarized metallic band
> structure (e.g., Ni.I
> notice in Example 8, that its band structure is
> "unpolarized" before
> applying bands_FS.x).  And sure enough, if you're
> dumb and try anyway, it
> abends with a read error, probably because there's
> twice the number of
> k-points out there that it expects.
> 
> If anyone out there wants to extend (or has
> extended) Eyvaz' code, I'd be a
> willing alpha-tester.  
> 
> Paul M. Grant, PhD
> Principal, W2AGZ Technologies
> Visiting Scholar, Applied Physics, Stanford
> University
> EPRI Science Fellow (Retired)
> IBM Research Staff Member Emeritus
> w2agz at pacbell.net
> http://www.w2agz.com
>  
>  
> 
> 
> > _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From yupiaofei at mail.sdu.edu.cn  Thu Dec 13 03:34:56 2007
From: yupiaofei at mail.sdu.edu.cn (yupiaofei(SDU))
Date: Thu, 13 Dec 2007 10:34:56 +0800
Subject: [Pw_forum] Optical properties
Message-ID: <397513651.07592@mail.sdu.edu.cn>



Hi, everybody!

I'm trying to perform a calculation for the optical properties of a bulk material. As we know, it can obtain it form the imaginary part of the dielectric constant. but I don't know if the PWSCF code could do this.

Have anybody done this before?



Kesong Yang

School of Physics and Microelectronics

Shandong University, Jinan 250100, People?s Republic of China


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From vietbacchemist at gmail.com  Thu Dec 13 07:04:16 2007
From: vietbacchemist at gmail.com (Viet Bac)
Date: Thu, 13 Dec 2007 15:04:16 +0900
Subject: [Pw_forum] Strange phonon branches appear in phonon dispersion
Message-ID: <ea64856c0712122204k6ba1942fmc9c4d7925d16b845@mail.gmail.com>

>
> Dear Dr. Stefano and Dr. Mohr,


Thank you for your  comments,

Actually I had successfully  done  phonon dispersion and  EPC  for Al bulk
structure with  good  results so from now I want to apply for the Al wires
structures. Firstly I calculate for 2 atom cell of Al with zigzag wires, and
I got 6 phonon modes along q-points and appear some negative frequencies, so
I tried to improve my calculation but always appear negative acoustic
frequencies (optical branch is no problem) and then I did with 4, 6 atom
cell and of course I got 3-n modes but my results still no good like I
expect. :(
To check my set up parameters I calculate the same procedure for Al 1D
linear chain with 1 and 2 atom cell with hopefully the phonon curves will be
the same as I studied theoretically in Solid States books, but it was not
:(. So should my calculation be wrong with this system. Could you give me
advice about my input parameters? Please keep your eyes my INPUT files (in
case of 2 atoms in zigzag chain)

Al.scf.fit.in

 &SYSTEM
                       ibrav = 6,
                 celldm(1) = 39.994,
                   celldm(3) =  0.199762906,
                         nat = 2,
                        ntyp = 1,
                     ecutwfc = 25.D0 ,
                     ecutrho = 300,
                 occupations = 'smearing' ,
                     degauss = 0.05 ,
                    smearing = 'methfessel-paxton' ,
                      la2F = .true.
 /
 &ELECTRONS
                    conv_thr = 1.D-10 ,
                 mixing_beta = 0.7D0 ,
 /
ATOMIC_SPECIES
   Al   26.98000  Al.vbc.UPF
ATOMIC_POSITIONS angstrom
Al       0.000000000   1.517315647   2.138739361
Al       0.000000000   0.116702849   0.023699809
K_POINTS automatic
  4 4 40   0 0 0

Al.scf.in

 &SYSTEM
                       ibrav = 6,
                 celldm(1) = 39.994,
                   celldm(3) =  0.199762906,
                         nat = 2,
                        ntyp = 1,
                     ecutwfc = 25.D0 ,
                     ecutrho = 300,
                 occupations = 'smearing' ,
                     degauss = 0.05 ,
                    smearing = 'methfessel-paxton'
 /
 &ELECTRONS
                    conv_thr = 1.D-10 ,
                 mixing_beta = 0.7D0 ,
 /
ATOMIC_SPECIES
   Al   26.98000  Al.vbc.UPF
ATOMIC_POSITIONS angstrom
Al       0.000000000   1.517315647   2.138739361
Al       0.000000000   0.116702849   0.023699809
K_POINTS automatic
  2 2 20   0 0 0

Al.elph.in

Electron-phonon coefficients for Alwire_2
 &inputph
  tr2_ph=1.0d-14,
  prefix='al2_elph',
  fildvscf='al2d',
  filelph='matrix'
  amass(1)=26.98,
  outdir='/root/tmp/',
  fildyn='al2m.dyn',
  elph=.true.,
  trans=.true.,
  ldisp=.true.
  nq1=1, nq2=1, nq3=10,

And hereafter 6 modes I got

 &plot nbnd=   6, nks=  27 /
            0.000000  0.000000  0.000000
   -0.0855   -0.0450    0.0000   20.7938  196.2309  372.4942
            0.000000  0.000000  0.100000
  -13.1432    5.6657    5.7114   20.3098  196.7060  372.0899
            0.000000  0.000000  0.200000
  -25.6753   10.2550   10.5805   18.8468  198.1533  371.0008
            0.000000  0.000000  0.300000
  -37.6999   14.0728   14.1858   16.2544  200.5950  369.4869
            0.000000  0.000000  0.400000
  -48.8295   11.6034   16.4265   16.4576  203.9728  367.7201
            0.000000  0.000000  0.500000
  -58.7192   -5.6944   16.7453   17.6129  208.1190  365.6663
            0.000000  0.000000  0.600000
  -67.0895  -15.3952   14.9673   18.4203  212.8051  363.1793
            0.000000  0.000000  0.700000
  -73.7443  -21.7038   11.9605   19.3942  217.8126  360.1938
            0.000000  0.000000  0.800000
  -78.6120  -26.9948    9.8326   20.4642  222.9635  356.8134
            0.000000  0.000000  0.900000
  -81.7857  -31.7595   10.1665   21.2176  228.1041  353.2106
            0.000000  0.000000  1.000000
  -83.4878  -36.1149   10.5785   21.4924  233.0809  349.4591
            0.000000  0.000000  1.100000
  -83.9637  -39.9380    6.4409   21.5912  237.7521  345.4939
            0.000000  0.000000  1.200000
  -83.3549  -43.0700  -11.8614   21.8643  242.0400  341.2345
            0.000000  0.000000  1.300000
  -81.7148  -45.5109  -19.5363   22.1233  245.9755  336.7214
            0.000000  0.000000  1.400000
  -79.2450  -47.4002  -24.2602   21.7049  249.6731  332.1110
            0.000000  0.000000  1.500000
  -76.4698  -48.7989  -26.8527   20.1426  253.2412  327.5276
            0.000000  0.000000  1.600000
  -74.0708  -49.5494  -28.8342   17.6459  256.7020  322.9460
            0.000000  0.000000  1.700000
  -72.4259  -49.4368  -31.6947   14.8469  259.9856  318.2672
            0.000000  0.000000  1.800000
  -71.2114  -48.4948  -35.6608   11.6256  263.0044  313.5063
            0.000000  0.000000  1.900000
  -69.6799  -47.0750  -39.7963    4.2536  265.7429  308.8670
            0.000000  0.000000  2.000000
  -67.4586  -45.5010  -43.2503  -12.7026  268.2849  304.5960
            0.000000  0.000000  2.100000
  -64.9647  -46.1360  -43.6300  -19.3793  270.7903  300.7406
            0.000000  0.000000  2.200000
  -63.0506  -49.2247  -40.9136  -23.4729  273.4711  297.0578
            0.000000  0.000000  2.300000
  -62.1609  -52.8376  -37.0315  -25.3558  276.5514  293.2015
            0.000000  0.000000  2.400000
  -61.8563  -56.2311  -32.5370  -26.2996  280.1674  289.0264
            0.000000  0.000000  2.500000
  -61.6387  -57.8617  -29.3445  -27.6304  283.8161  285.1565
            0.000000  0.000000  2.503000
  -61.6384  -57.8633  -29.3391  -27.6341  283.8284  285.1440


   Bac,

------------------------------
Phung Viet Bac
Division of Mathematical and Physical Science,
Graduate School of Natural Science and Technology,
Kanazawa University,
Kakuma, Kanazawa 920-1192, JAPAN








>
> your phonon branches are really strange...
> with two atoms I would expect 6 modes per each q-point
>
> stefano
>
>
>
> 6 branches for 2 atom are what one expects (in general 3n branches and 3
> acoustical and 3n-3 optical ones).
>
> However negative values indicate some error in your calculation, dependent
> on the magnitude and system.
> You can impose some sum-rules for the acoustic ones, to force them to be
> 0 at the Gamma point.
>
> Acoustic forces are harder to calculate (smaller forces). In your case I
> would guess up to 15 cm^1 should be ok for the acoustic ones.
> Negative optical ones should not occur.
>
> Best
> Marcel Mohr
>
>
>
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From hqzhou at nju.edu.cn  Thu Dec 13 07:56:01 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Thu, 13 Dec 2007 14:56:01 +0800
Subject: [Pw_forum] bands_FS.x and spin polarized metals
References: <000001c83cfe$26acd5c0$74068140$@net><11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it><47604B86.8070207@mit.edu>
	<B5FACEDA-2DA5-4DD4-B3B2-0C1D243B7A6B@nest.sns.it>
Message-ID: <003d01c83d55$390fa420$1d00a8c0@solarflare>

Wow, what a "home computer"! Moor's law hadn't been invented 
at that time, right? :-)

Are there any copyright issue to prevent me from using it in my 
presentation about "concise history of personal computer"?

Thanks for sharing the precious picture with us!

Huiqun Zhou
@Earth Sciences, Nanjing University, China

----- Original Message ----- 
From: "Paolo Giannozzi" <giannozz at nest.sns.it>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Thursday, December 13, 2007 5:12 AM
Subject: Re: [Pw_forum] bands_FS.x and spin polarized metals


> 
> On Dec 12, 2007, at 21:58 , Nicola Marzari wrote:
> 
>>> I am old enough to have seen card punchers in action, so the term
>>> "abend" is not unknown to me, but I guess younger people don't
>>> know that it is a shorthand for "abnormal end", on IBM mainframes...
>>
>> What's a mainframe ? Is it like a really, really big ipod ?
> 
> do you remember the picture of the "home computer
> in 2004" you sent me some time ago ?
> http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg
> :-)
> 
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
> 
> 
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>

From w2agz at pacbell.net  Thu Dec 13 08:40:56 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Wed, 12 Dec 2007 23:40:56 -0800
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
Message-ID: <002201c83d5b$7f75e450$7e61acf0$@net>

To All (especially Paolo, Nicola, Matteo and Axel):

I?m in the middle of attempting, as an exercise, the calculation of the
electronic structure of monoclinic CuO (tenorite) within the LDA+U
provisions of PWscf (Cu is on the ?approved list? of elements contained in
set_hubbard_l.f90 and tabd.f90).  FeO and NiO I get to go OK, but CuO is
giving me problems.  Tenorite is a well-established AF Hubbard-type
insulator, and the LDA+U approach can yield a supportive band structure
(e.g., see JPCM 11, 5021 (1999) and references therein).  However, I am not
aware of an LDA+U calculation starting from a PW/PP formalism for tenorite.
If one exists, please send me the reference and ignore the rest of this
posting.

Simplistically, the initial d-state configuration of Cu2+ in CuO by Hund?s
Rule should be 3d9 (one empty minority spin state state
a hole).   But, with
nspin=2, lda_plus_u set true, and U=5 eV (arbitrary), the initial minority
spin occupation gets set to unity, not 4/5 on average (3/5 for Ni and 1/5
for Fe).  Is this due to occ_loc being set to 10 in tabd.f90 and not 9 (it?s
6 for Fe and 8 for Ni)?  The occupation distribution converges to around
0.92 for eg and 0.99 for t2g with self-consistency, a metallic state, and no
amount of ?alternative user ns eigenvalue guidance? gives a gap.  I haven?t
tried any Wannier projections
rich man?s or poor
yet, because I suspect
there is another issue
choice of the proper Cu PP.

The choice of Cu pseudopotentials available in the PWscf library are rather
limited and weird
at least to my na?ve and limited experience.  I have been
using primarily the Perdew-Zunger  LDA PP, Cu.pz-n-van_ak.UPF, computed with
valence orbital occupations 3d9.5, 4s1.0 and 4p0.5 (!) (the PW91 and PBE
functionals have equivalent occupations and give similar results).  When I
try Cu.pz-d-rrkjus.UPF, with 3d10, 4s1 and 4p-1(!!!), the first scf
iteration yields individual spin occupations of nearly 5(!!!), and the
situation gets really ugly thereafter.

Why aren?t there Cu PPs with occupations 3d10, 4s1, or even 3d9, 4s2?  I?ve
spent the afternoon studying Paolo?s guide to PP generation and would be
willing to give these a try if that would help
but I sorely need some
advice.  I?ve also been looking over David Vanderbilt?s web site and found
this bit of wisdom:  ?Choosing the method of pseudizing the local
potential
This is something of a black art?.

-Paul

PS
there is something truly marvelous and mysterious about the CuO double
bond
it?s given us high temperature superconductivity.  But 21 years later,
there?s no general agreement on wherein and why it arises.

PPS
Is there a utility somewhere that plots the radial dependence of V(r)
and/or rho(r) of a given PP?

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


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From efeomer76 at gmail.com  Thu Dec 13 08:54:11 2007
From: efeomer76 at gmail.com (=?ISO-8859-1?Q?=D6mer_Ko=E7?=)
Date: Thu, 13 Dec 2007 09:54:11 +0200
Subject: [Pw_forum] IFC's and eigendisplacements in example06
Message-ID: <75810c7f0712122354o3de01076t3168b04777e92734@mail.gmail.com>

Dear PWSCF users,


My questions are about example06

 1) Could you give me some analysis and explanations on the range of the
interatomic force constants (IFC's) for AlAs in example06.
 On the Forum, there are  some informations and explanations but i don't
understand them. I need more explanations.



alas444.fc



  2     2  2 10.5000000  0.0000000  0.0000000  0.0000000   0.0000000
0.0000000

           1   'Al '    24590.7655930491

           2   'As '    68285.4024548272

    1     1      0.0000000      0.0000000      0.0000000

    2     2      0.2500000      0.2500000      0.2500000

 T

     13.7439581       0.0000000      0.0000000

      0.0000000      13.7439581      0.0000000

      0.0000000       0.0000000     13.7439581

    1

      2.5582103       0.0000000      0.0000000

      0.0000000       2.5582103      0.0000000

      0.0000000       0.0000000      2.5582103

    2

     -2.5582103       0.0000000      0.0000000

      0.0000000      -2.5582103      0.0000000

      0.0000000       0.0000000     -2.5582103

   4    4   4

   1    1   1   1

   1    1   1   2.17004984418E-01

   2    1   1  -5.06952740903E-03

   3    1   1   9.99492789182E-05

   4    1   1  -5.06952740903E-03

   1    2   1   1.07967422105E-02

   2    2   1  -6.07584921925E-04

   3    2   1  -1.61474518909E-04

   4    2   1  -5.06952740903E-03

   1    3   1   4.18136269798E-03

   2    3   1  -6.07584921925E-04

   3    3   1   9.99492789182E-05

   4    3   1  -6.07584921925E-04

   1    4   1   1.07967422105E-02

   2    4   1  -5.06952740903E-03

   3    4   1  -1.61474518909E-04

   4    4   1  -6.07584921925E-04

   1    1   2  -5.06952740903E-03

   2    1   2  -1.61474518909E-04

   3    1   2  -6.07584921925E-04

   ????????????????????????????




2) Is there a meaning of ratio of displacement of the two ions (Al and As)
in the eigendisplacement pattern?
The calculated vibrational eigenvectors at X point are below. How can we
evaluate this data?



q =       0.0000       0.0000      1.0000

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

     omega( 1) =        2.841119 [THz] =      94.770143 [cm-1]

 (   0.611885   0.039292    -0.353070  -0.018348     0.000000    0.000000
) Al

 ( -0.352406   -0.018313     0.610733   0.039218     0.000000   0.000000    )
As

     omega( 2) =        2.841119 [THz] =      94.770143 [cm-1]

 (   0.353530   0.003400     0.613143  -0.001588      0.000000    0.000000
)

 (   0.611989  -0.001585     0.352865   0.003394     0.000000    0.000000
)

     omega( 3) =        6.563802 [THz] =     218.946309 [cm-1]

 (   0.000000   0.000000     0.000000   0.000000     0.000000    0.000000
)

 (   0.000000   0.000000     0.000000   0.000000     1.000000    0.000000
)

     omega( 4) =       10.442067 [THz] =     348.312171 [cm-1]

 (   0.753056   0.016289    -0.563430   0.002731     0.000000    0.000000
)

 (   0.203284  -0.000985    -0.271700  -0.005877     0.000000    0.000000
)

     omega( 5) =       10.442067 [THz] =     348.312171 [cm-1]

 ( -0.563178   -0.017050    -0.753227  -0.002855     0.000000   0.000000
)

 (   0.271762   0.001030     0.203193   0.006152     0.000000    0.000000
)

     omega( 6) =       12.209736 [THz] =     407.275646 [cm-1]

 (   0.000000   0.000000     0.000000   0.000000    -0.138259    0.990396
)

 (   0.000000   0.000000     0.000000   0.000000     0.000000    0.000000
)

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

     diagonalizing the dynamical matrix ...

Many thanks in advance

?mer.

-- 
?mer Ko?
100. Y?l University
Dept of Physics Van, Turkey
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From benassi.a at gmail.com  Thu Dec 13 09:03:52 2007
From: benassi.a at gmail.com (Andrea Benassi)
Date: Thu, 13 Dec 2007 00:03:52 -0800
Subject: [Pw_forum] Optical properties
In-Reply-To: <397513651.07592@mail.sdu.edu.cn>
References: <397513651.07592@mail.sdu.edu.cn>
Message-ID: <97c430b70712130003p3663b054nbe2704c319a363a4@mail.gmail.com>

Hi Kesong,
you can find a post processing named epsilon.f90, you have to compile it
separately doing "make epsilon.x" from the PP folder. In the DOCS folder you
can also find a manual that explane how the code works and all the possible
options.
Let me know if you face some problems.
best regards.
Andrea


-- 
Andrea Benassi
National Research Center S3, CNR-INFM  ( http://www.s3.infm.it )
Dipartimento di Fisica, Universita' di Modena e Reggio Emilia
Via Campi 213/A I-41100 Modena, Italy
Tel:     +39 059 2055314
Fax:     +39 059 374794
E-mail:  benassi.andrea at unimore.it
URL:     http://www.nanoscience.unimo.it
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From njuxuyuehua at gmail.com  Thu Dec 13 09:06:40 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 13 Dec 2007 16:06:40 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
Message-ID: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>

hi all:
in relax ,i do not want to write wavefuntion into disk.for there is no
enough space and time wasting.
can anyone to tell me how to deal with it ?

thank you in advance
-- 
Xu Yuehua
physics Department of Nanjing university
China
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From marcel at physik.tu-berlin.de  Thu Dec 13 11:02:58 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Thu, 13 Dec 2007 11:02:58 +0100 (CET)
Subject: [Pw_forum] Strange phonon branches appear in phonon dispersion
In-Reply-To: <ea64856c0712122204k6ba1942fmc9c4d7925d16b845@mail.gmail.com>
References: <ea64856c0712122204k6ba1942fmc9c4d7925d16b845@mail.gmail.com>
Message-ID: <20071213102451.S83566@rosa.physik-pool.tu-berlin.de>

>>
>> Dear Dr. Stefano and Dr. Mohr,
 			^^
That is too much honour for me as I am still working on these two letters.

The input below looks ok for me, but two things:

1.) for electronic wavefunctions you choose a 4 4 40 grid. It should be no 
difference to a 1 1 40 one (because of 1 dim, there are no bloch waves 
perp to your wire axis)

2.) your   tr2_ph=1.0d-14 is maybe too small. try to use a value around 
1.0d-20

What about the convergence of the other parameters (ecutwfc)
with respect to your phonon frequencies?

Maybe you find some information in the paper verstraete PhysRevB 74 153408 
(2006).


Best Marcel


>
>
> Thank you for your  comments,
>
> Actually I had successfully  done  phonon dispersion and  EPC  for Al bulk
> structure with  good  results so from now I want to apply for the Al wires
> structures. Firstly I calculate for 2 atom cell of Al with zigzag wires, and
> I got 6 phonon modes along q-points and appear some negative frequencies, so
> I tried to improve my calculation but always appear negative acoustic
> frequencies (optical branch is no problem) and then I did with 4, 6 atom
> cell and of course I got 3-n modes but my results still no good like I
> expect. :(
> To check my set up parameters I calculate the same procedure for Al 1D
> linear chain with 1 and 2 atom cell with hopefully the phonon curves will be
> the same as I studied theoretically in Solid States books, but it was not
> :(. So should my calculation be wrong with this system. Could you give me
> advice about my input parameters? Please keep your eyes my INPUT files (in
> case of 2 atoms in zigzag chain)
>
> Al.scf.fit.in
>
> &SYSTEM
>                       ibrav = 6,
>                 celldm(1) = 39.994,
>                   celldm(3) =  0.199762906,
>                         nat = 2,
>                        ntyp = 1,
>                     ecutwfc = 25.D0 ,
>                     ecutrho = 300,
>                 occupations = 'smearing' ,
>                     degauss = 0.05 ,
>                    smearing = 'methfessel-paxton' ,
>                      la2F = .true.
> /
> &ELECTRONS
>                    conv_thr = 1.D-10 ,
>                 mixing_beta = 0.7D0 ,
> /
> ATOMIC_SPECIES
>   Al   26.98000  Al.vbc.UPF
> ATOMIC_POSITIONS angstrom
> Al       0.000000000   1.517315647   2.138739361
> Al       0.000000000   0.116702849   0.023699809
> K_POINTS automatic
>  4 4 40   0 0 0
>
> Al.scf.in
>
> &SYSTEM
>                       ibrav = 6,
>                 celldm(1) = 39.994,
>                   celldm(3) =  0.199762906,
>                         nat = 2,
>                        ntyp = 1,
>                     ecutwfc = 25.D0 ,
>                     ecutrho = 300,
>                 occupations = 'smearing' ,
>                     degauss = 0.05 ,
>                    smearing = 'methfessel-paxton'
> /
> &ELECTRONS
>                    conv_thr = 1.D-10 ,
>                 mixing_beta = 0.7D0 ,
> /
> ATOMIC_SPECIES
>   Al   26.98000  Al.vbc.UPF
> ATOMIC_POSITIONS angstrom
> Al       0.000000000   1.517315647   2.138739361
> Al       0.000000000   0.116702849   0.023699809
> K_POINTS automatic
>  2 2 20   0 0 0
>
> Al.elph.in
>
> Electron-phonon coefficients for Alwire_2
> &inputph
>  tr2_ph=1.0d-14,
>  prefix='al2_elph',
>  fildvscf='al2d',
>  filelph='matrix'
>  amass(1)=26.98,
>  outdir='/root/tmp/',
>  fildyn='al2m.dyn',
>  elph=.true.,
>  trans=.true.,
>  ldisp=.true.
>  nq1=1, nq2=1, nq3=10,
>
> And hereafter 6 modes I got
>
> &plot nbnd=   6, nks=  27 /
>            0.000000  0.000000  0.000000
>   -0.0855   -0.0450    0.0000   20.7938  196.2309  372.4942
>            0.000000  0.000000  0.100000
>  -13.1432    5.6657    5.7114   20.3098  196.7060  372.0899
>            0.000000  0.000000  0.200000
>  -25.6753   10.2550   10.5805   18.8468  198.1533  371.0008
>            0.000000  0.000000  0.300000
>  -37.6999   14.0728   14.1858   16.2544  200.5950  369.4869
>            0.000000  0.000000  0.400000
>  -48.8295   11.6034   16.4265   16.4576  203.9728  367.7201
>            0.000000  0.000000  0.500000
>  -58.7192   -5.6944   16.7453   17.6129  208.1190  365.6663
>            0.000000  0.000000  0.600000
>  -67.0895  -15.3952   14.9673   18.4203  212.8051  363.1793
>            0.000000  0.000000  0.700000
>  -73.7443  -21.7038   11.9605   19.3942  217.8126  360.1938
>            0.000000  0.000000  0.800000
>  -78.6120  -26.9948    9.8326   20.4642  222.9635  356.8134
>            0.000000  0.000000  0.900000
>  -81.7857  -31.7595   10.1665   21.2176  228.1041  353.2106
>            0.000000  0.000000  1.000000
>  -83.4878  -36.1149   10.5785   21.4924  233.0809  349.4591
>            0.000000  0.000000  1.100000
>  -83.9637  -39.9380    6.4409   21.5912  237.7521  345.4939
>            0.000000  0.000000  1.200000
>  -83.3549  -43.0700  -11.8614   21.8643  242.0400  341.2345
>            0.000000  0.000000  1.300000
>  -81.7148  -45.5109  -19.5363   22.1233  245.9755  336.7214
>            0.000000  0.000000  1.400000
>  -79.2450  -47.4002  -24.2602   21.7049  249.6731  332.1110
>            0.000000  0.000000  1.500000
>  -76.4698  -48.7989  -26.8527   20.1426  253.2412  327.5276
>            0.000000  0.000000  1.600000
>  -74.0708  -49.5494  -28.8342   17.6459  256.7020  322.9460
>            0.000000  0.000000  1.700000
>  -72.4259  -49.4368  -31.6947   14.8469  259.9856  318.2672
>            0.000000  0.000000  1.800000
>  -71.2114  -48.4948  -35.6608   11.6256  263.0044  313.5063
>            0.000000  0.000000  1.900000
>  -69.6799  -47.0750  -39.7963    4.2536  265.7429  308.8670
>            0.000000  0.000000  2.000000
>  -67.4586  -45.5010  -43.2503  -12.7026  268.2849  304.5960
>            0.000000  0.000000  2.100000
>  -64.9647  -46.1360  -43.6300  -19.3793  270.7903  300.7406
>            0.000000  0.000000  2.200000
>  -63.0506  -49.2247  -40.9136  -23.4729  273.4711  297.0578
>            0.000000  0.000000  2.300000
>  -62.1609  -52.8376  -37.0315  -25.3558  276.5514  293.2015
>            0.000000  0.000000  2.400000
>  -61.8563  -56.2311  -32.5370  -26.2996  280.1674  289.0264
>            0.000000  0.000000  2.500000
>  -61.6387  -57.8617  -29.3445  -27.6304  283.8161  285.1565
>            0.000000  0.000000  2.503000
>  -61.6384  -57.8633  -29.3391  -27.6341  283.8284  285.1440
>
>
>   Bac,
>
> ------------------------------
> Phung Viet Bac
> Division of Mathematical and Physical Science,
> Graduate School of Natural Science and Technology,
> Kanazawa University,
> Kakuma, Kanazawa 920-1192, JAPAN
>
>
>
>
>
>
>
>
>>
>> your phonon branches are really strange...
>> with two atoms I would expect 6 modes per each q-point
>>
>> stefano
>>
>>
>>
>> 6 branches for 2 atom are what one expects (in general 3n branches and 3
>> acoustical and 3n-3 optical ones).
>>
>> However negative values indicate some error in your calculation, dependent
>> on the magnitude and system.
>> You can impose some sum-rules for the acoustic ones, to force them to be
>> 0 at the Gamma point.
>>
>> Acoustic forces are harder to calculate (smaller forces). In your case I
>> would guess up to 15 cm^1 should be ok for the acoustic ones.
>> Negative optical ones should not occur.
>>
>> Best
>> Marcel Mohr
>>
>>
>>
>


From marcel at physik.tu-berlin.de  Thu Dec 13 11:14:16 2007
From: marcel at physik.tu-berlin.de (Marcel Mohr)
Date: Thu, 13 Dec 2007 11:14:16 +0100 (CET)
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <003d01c83d55$390fa420$1d00a8c0@solarflare>
References: <000001c83cfe$26acd5c0$74068140$@net><11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it><47604B86.8070207@mit.edu>
	<B5FACEDA-2DA5-4DD4-B3B2-0C1D243B7A6B@nest.sns.it>
	<003d01c83d55$390fa420$1d00a8c0@solarflare>
Message-ID: <20071213111001.N83566@rosa.physik-pool.tu-berlin.de>

On Thu, 13 Dec 2007, Huiqun Zhou wrote:

> Wow, what a "home computer"! Moor's law hadn't been invented
> at that time, right? :-)
> Are there any copyright issue to prevent me from using it in my
> presentation about "concise history of personal computer"?

Although I liked it very much, too. I showed it to a colleague and he told 
me it is fake.

It is a picture of a sumbarine control station see 
http://www.snopes.com/inboxer/hoaxes/computer.asp

Sorry for being the spoiler
Marcel



>
>
> Thanks for sharing the precious picture with us!
>
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
> ----- Original Message -----
> From: "Paolo Giannozzi" <giannozz at nest.sns.it>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Thursday, December 13, 2007 5:12 AM
> Subject: Re: [Pw_forum] bands_FS.x and spin polarized metals
>
>
>>
>> On Dec 12, 2007, at 21:58 , Nicola Marzari wrote:
>>
>>>> I am old enough to have seen card punchers in action, so the term
>>>> "abend" is not unknown to me, but I guess younger people don't
>>>> know that it is a shorthand for "abnormal end", on IBM mainframes...
>>>
>>> What's a mainframe ? Is it like a really, really big ipod ?
>>
>> do you remember the picture of the "home computer
>> in 2004" you sent me some time ago ?
>> http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg
>> :-)
>>
>> 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
>>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


From ezadshojaee at hotmail.com  Thu Dec 13 11:18:48 2007
From: ezadshojaee at hotmail.com (Ezad Shojaee)
Date: Thu, 13 Dec 2007 10:18:48 +0000
Subject: [Pw_forum] FW: about Fermi Energy shift in periodic (q=0)
 perturbations
In-Reply-To: <47570D81.70305@sissa.it>
References: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>
	<47570D81.70305@sissa.it>
Message-ID: <BLU120-W153640BC01491BDBB46138AA660@phx.gbl>


 
Dear Mr. Gironcoli
Thanx for your answer, but sorry I'm not sure i follow you, could you open it more?!
you mean in the case of periodic perturbation(like the constant one) we have a change in the # of electrons? what exactly happens in this case, so we have to shift the Fermi energy(in order to have neutrality condition)? What happens if we do not shift it(As you see i want you to answer the question you made!)?
Thanx again
 
Ezad Shojaee - Tehran University
 
> At any q/=0 the perturbation is such that the number of electrons does > not change.> Even in the limit of q->0 the macroscopic term in the density response > is zero (because in a metal> the dielectic constant is infinite).> Now consider the case of a periodic (q=0) perturbation, the simplest > one, a constant, threated with or w/o the FE shift... which of the two > treatments corresponds to the result you would obtain in the liimit q->0 ?
___________________________________________> 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  Thu Dec 13 11:26:02 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 13 Dec 2007 11:26:02 +0100 (CET)
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
Message-ID: <2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>


On Thu, December 13, 2007 09:06, xu yuehua wrote:
> hi all:
> in relax ,i do not want to write wavefuntion into disk.for there is no
> enough space and time wasting.
> can anyone to tell me how to deal with it ?

I think setting disk_io='none' in the &control namelist should do the
trick, but are you sure it is a good idea?


-- 
Lorenzo Paulatto
+39 040 3787 511
http://people.sissa.it/~paulatto/


----------------------------------------------------------------
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From degironc at sissa.it  Thu Dec 13 11:47:15 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 13 Dec 2007 11:47:15 +0100
Subject: [Pw_forum] FW: about Fermi Energy shift in periodic (q=0)
	perturbations
In-Reply-To: <BLU120-W153640BC01491BDBB46138AA660@phx.gbl>
References: <BLU120-W17CDF637275211EE95DF6AA6D0@phx.gbl>	<47570D81.70305@sissa.it>
	<BLU120-W153640BC01491BDBB46138AA660@phx.gbl>
Message-ID: <47610DB3.7020700@sissa.it>

we are interested in the limit for q->0.

in this limit the total number of electrons does not change and the 
Fermi energy does not shift (since it is a q/=0 calculation) however the
delta_n(q) = \sum_G chi(q,q+G) deltaV_0(q+G)
                 = \sum_G chi0(q,q+G) [deltaV_0(q+G) + 4pi/(q+G)^2 
delta_n(q+G)]

Now chi0(q,q) for metals is FINITE in the limit of q->0 (related to the 
DOS at the FE) and 4pi/q**2 explodes thus the only way things can still 
satisfy the above relation is that n(q) -> 0 quadratically so that
1) the limit for 4pi/q**2 delta_n(q) gives a FINITE contibution to the 
potential V_scf(q->0) that toghether with the other component of the 
response makes that
2) the system is neutral ... i.e. n(q)->0.

In a q==0 calculation the FINITE value of V_scf(q=0) coming from the 
Coulomb potential cannot be calculated calculated directly from 
condition 1) since q==0 and the above ratio is ill defined but can be 
determined by condition 2) ... whether you want to call it a potential 
shift or an (opposite) FE shift is up to you. This latter choice is made 
in the phonon code.

Hope this helps,

 stefano


Ezad Shojaee wrote:
>
> Dear Mr. Gironcoli
>
> Thanx for your answer, but sorry I'm not sure i follow you, could you 
> open it more?!
>
> you mean in the case of periodic perturbation(like the constant one) 
> we have a change in the # of electrons? what exactly happens in this 
> case, so we have to shift the Fermi energy(in order to have neutrality 
> condition)? What happens if we do not shift it(As you see i want you 
> to answer the question you made!)?
>
> Thanx again
>
>  
> Ezad Shojaee - Tehran University
>  
>
> > At any q/=0 the perturbation is such that the number of electrons does
> > not change.
> > Even in the limit of q->0 the macroscopic term in the density response
> > is zero (because in a metal
> > the dielectic constant is infinite).
> > Now consider the case of a periodic (q=0) perturbation, the simplest
> > one, a constant, threated with or w/o the FE shift... which of the two
> > treatments corresponds to the result you would obtain in the liimit 
> q->0 ?
>
> ___________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> ------------------------------------------------------------------------
> Express yourself instantly with MSN Messenger! MSN Messenger 
> <http://clk.atdmt.com/AVE/go/onm00200471ave/direct/01/>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From baroni at sissa.it  Thu Dec 13 13:02:53 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 13 Dec 2007 12:02:53 +0000
Subject: [Pw_forum] about the precision of energy and some extend
	problem.
In-Reply-To: <Pine.LNX.4.44.0712121405530.23154-101000@newton.physics.metu.edu.tr>
References: <Pine.LNX.4.44.0712121405530.23154-101000@newton.physics.metu.edu.tr>
Message-ID: <0E5CF085-9665-4032-93B7-D9916AC68FD1@sissa.it>

Dear all: two further comments.

1) I have not seen in detail the output of Xu Yuehua's calculations,  
but I would like to point out that one may have negative frequencies  
even if the atomic forces and crystal stress vanish. Negative  
frequencies are a manifestation of a mechanical instability that may  
occur even when the first derivatives of the energy with respect to  
any possible mechanical distortion of the lattice vanish.

2) I am not myself a native English speaker, and I know by experience  
how much it takes to write in a foreign language. I am also aware that  
the difficulty of writing decent English depends a lot on one's own  
mother tongue. However, I would like to kindly urge contributors to  
this mailing list to read twice their posts and always ask themselves  
very carefully if what they have written can be understood with a fair  
investment of time and attention. Working on one's own way of  
expressing oneself is a very important (and rewarding, rest assured!)  
exercise that non-native English speakers should do.

Best wishes,
SB

On Dec 12, 2007, at 12:11 PM, Hande Ustunel wrote:

> Dear Xu Yuehua,
>
> You should fit your energies to a parabola and find the minimum of the
> fit. For a second order fit, your minimum is at about 2.83. 2.77 is  
> just a
> local blip in your rather jumpy data. You cannot decide by looking  
> at the
> individual energies because they do not follow a smooth function.  
> But even
> for the "wrong" lattice constant, there's no physical reason why you  
> should
> get negative frequencies if you have converged your electronic and  
> atomic
> coordinates to high accuracy. I'm attaching the fit as an example.
>
> I would also suggest increasing your cutoff a little because your  
> data, as
> I said, is a bit noisy near the minimum.
>
> Best,
> Hande
>
> On Wed, 12 Dec 2007, xu yuehua wrote:
>
>> hi ,uesers here :
>> i relax one crystal lattice vs energy:
>> i have compute several energy list :
>>
>> c          E(RY)
>> 2.795  -137.79266
>> 2.78   -137.79248
>> 2.77   -137.79233
>> 2.8     -137.7927
>> 2.81  -137.79275
>> 2.82  -137.79275
>> 2.83  -137.79278
>> 2.84  -137.79276
>> 2.85  -137.79279
>> 2.86  -137.79272
>> 2.87  -137.79265
>> 2.88  -137.79258
>> 2.9   -137.79229
>> 2.95  -137.79122
>> these energy points are smooth and  can be plotted  parabola.
>> the system has 12 atoms.the energy is different most at the third  
>> digit
>> after radix point. so i think the average energy/atom is less 0.0001.
>>
>> i want to ask  the  within the precision of energy(my thinking is  
>> based on
>> that :my above calculation is set ecutwfc:29, ecutrho:200,and the   
>> criterion
>> is 35,350, the convergence is 0.0049345 ry.)
>> so this small difference of energy can skip,i.e we can choose 2.77  
>> which is
>> regarded as the best structure?
>> as why i ask this question,for the the structure of 2.85 has two  big
>> negative frequencies  near -100cm-1, even if i add asr .
>> but 2.77 has no negative frequency after i add asr.
>>
>>
>>
>
> -- 
> Hande Ustunel
> Department of Physics
> Office 439
> Middle East Technical University
> Ankara 06531, Turkey
> Tel : +90 312 210 3264
> http://www.physics.metu.edu.tr/~hande
> <fit.eps>_______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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



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From baroni at sissa.it  Thu Dec 13 13:10:11 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 13 Dec 2007 12:10:11 +0000
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <20071213111001.N83566@rosa.physik-pool.tu-berlin.de>
References: <000001c83cfe$26acd5c0$74068140$@net><11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it><47604B86.8070207@mit.edu>
	<B5FACEDA-2DA5-4DD4-B3B2-0C1D243B7A6B@nest.sns.it>
	<003d01c83d55$390fa420$1d00a8c0@solarflare>
	<20071213111001.N83566@rosa.physik-pool.tu-berlin.de>
Message-ID: <69A8BBD9-76A5-49D1-B1B8-41DB53B40546@sissa.it>

happily enough, different people have a different sense of humor!
i enjoyed very much this thread.
best wishes to you all
S.

On Dec 13, 2007, at 10:14 AM, Marcel Mohr wrote:

> On Thu, 13 Dec 2007, Huiqun Zhou wrote:
>
>> Wow, what a "home computer"! Moor's law hadn't been invented
>> at that time, right? :-)
>> Are there any copyright issue to prevent me from using it in my
>> presentation about "concise history of personal computer"?
>
> Although I liked it very much, too. I showed it to a colleague and  
> he told
> me it is fake.
>
> It is a picture of a sumbarine control station see
> http://www.snopes.com/inboxer/hoaxes/computer.asp
>
> Sorry for being the spoiler
> Marcel
>
>
>
>>
>>
>> Thanks for sharing the precious picture with us!
>>
>> Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>>
>> ----- Original Message -----
>> From: "Paolo Giannozzi" <giannozz at nest.sns.it>
>> To: "PWSCF Forum" <pw_forum at pwscf.org>
>> Sent: Thursday, December 13, 2007 5:12 AM
>> Subject: Re: [Pw_forum] bands_FS.x and spin polarized metals
>>
>>
>>>
>>> On Dec 12, 2007, at 21:58 , Nicola Marzari wrote:
>>>
>>>>> I am old enough to have seen card punchers in action, so the term
>>>>> "abend" is not unknown to me, but I guess younger people don't
>>>>> know that it is a shorthand for "abnormal end", on IBM  
>>>>> mainframes...
>>>>
>>>> What's a mainframe ? Is it like a really, really big ipod ?
>>>
>>> do you remember the picture of the "home computer
>>> in 2004" you sent me some time ago ?
>>> http://www.fisica.uniud.it/~giannozz/public/pc2004.jpg
>>> :-)
>>>
>>> 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
>>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://www.democritos.it/mailman/listinfo/pw_forum
>>
>>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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



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From glaweh at physik.fu-berlin.de  Thu Dec 13 13:26:53 2007
From: glaweh at physik.fu-berlin.de (Henning Glawe)
Date: Thu, 13 Dec 2007 13:26:53 +0100
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <002201c83d5b$7f75e450$7e61acf0$@net>
References: <002201c83d5b$7f75e450$7e61acf0$@net>
Message-ID: <20071213122653.GA8219@physik.fu-berlin.de>

On Wed, Dec 12, 2007 at 11:40:56PM -0800, Paul M. Grant wrote:
> Simplistically, the initial d-state configuration of Cu2+ in CuO by Hund?s
> Rule should be 3d9 (one empty minority spin state state
a hole).   But, with
> nspin=2, lda_plus_u set true, and U=5 eV (arbitrary), the initial minority
> spin occupation gets set to unity, not 4/5 on average (3/5 for Ni and 1/5
> for Fe).  Is this due to occ_loc being set to 10 in tabd.f90 and not 9 (it?s
> 6 for Fe and 8 for Ni)?  The occupation distribution converges to around

as the d shell can be filled with 10 electrons, getting a initial hole into the 
d shell while occ_loc=10 is IMHO impossible.


> functionals have equivalent occupations and give similar results).  When I
> try Cu.pz-d-rrkjus.UPF, with 3d10, 4s1 and 4p-1(!!!), the first scf
> iteration yields individual spin occupations of nearly 5(!!!), and the
> situation gets really ugly thereafter.

I also encountered this problem with this pseudo potential; the problem lies
in the normalization of the 3d wave functions saved in the pp file. if you
search in the archives of the pw forum, you will find a patch for pwscf
allowing to recalculate the norm of the atomic states after the pp file has
been read.

-- 
c u
henning

From njuxuyuehua at gmail.com  Thu Dec 13 13:42:37 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 13 Dec 2007 20:42:37 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
Message-ID: <aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>

yes,maybe once i set  disk_io="none" ,when something goes wrong ,like power
is off suddenly,you have to start from  scratch .from this point ,it is
wasting time in deed.
but is there  an better idea ?
i am wondering


2007/12/13, Lorenzo Paulatto <paulatto at sissa.it>:
>
>
> On Thu, December 13, 2007 09:06, xu yuehua wrote:
> > hi all:
> > in relax ,i do not want to write wavefuntion into disk.for there is no
> > enough space and time wasting.
> > can anyone to tell me how to deal with it ?
>
> I think setting disk_io='none' in the &control namelist should do the
> trick, but are you sure it is a good idea?
>
>
> --
> Lorenzo Paulatto
> +39 040 3787 511
> http://people.sissa.it/~paulatto/
>
>
> ----------------------------------------------------------------
> 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
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From paulatto at sissa.it  Thu Dec 13 14:16:01 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 13 Dec 2007 14:16:01 +0100 (CET)
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
Message-ID: <8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>


On Thu, December 13, 2007 13:42, xu yuehua wrote:
> yes,maybe once i set  disk_io="none" ,when something goes wrong ,like
> power
> is off suddenly,you have to start from  scratch .from this point ,it is
> wasting time in deed.
> but is there  an better idea ?
> i am wondering

I think it is highly unlikely that you have more RAM than disk space, so
disk space should be no issue. Furthermore it should not be so slow, as
long as you are leaving wfc_collect=.false. which is the default.


From njuxuyuehua at gmail.com  Thu Dec 13 15:06:46 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Thu, 13 Dec 2007 22:06:46 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
	<8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
Message-ID: <aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>

thank you for your detailed analysis.  your guess is right .my outdir is set
to a place,not local to the nodes.i know the reason of my slow job,although
i did not know it through.
as for how to use a local directory as outdir ,it seems another new thing
for me.
would it be possible to tell me about that ?
thank you in advance



your sincerely
 xuyuehua

2007/12/13, Lorenzo Paulatto <paulatto at sissa.it>:
>
>
> On Thu, December 13, 2007 13:42, xu yuehua wrote:
> > yes,maybe once i set  disk_io="none" ,when something goes wrong ,like
> > power
> > is off suddenly,you have to start from  scratch .from this point ,it is
> > wasting time in deed.
> > but is there  an better idea ?
> > i am wondering
>
> I think it is highly unlikely that you have more RAM than disk space, so
> disk space should be no issue. Furthermore it should not be so slow, as
> long as you are leaving wfc_collect=.false. which is the default.
>
> From these assumptions I can guess that you are using a network share as
> temporary directory for your calculation; in other words your outdir is
> set to some place, probably in you home directory, which is not local to
> nodes but stays on a server and is shared via NFS (network file system).
>
> If this is your case, every time wavefunctions are written the data has to
> pass trough the network, it is somehow equivalent to collect_wfc=.true.
> but done externally by the operating system. Furthermore if you are using
> the same network for NFS and mpi when the traffic from NFS suddenly bursts
> it is likely to conflict with mpi and slow it down a lot.
>
> To avoid this problem you must use a local directory as outdir (like
> /tmp), but you to have to remember that if you want to restart a job you
> have to use exactly the same node you used before in order for them to
> find their wavefunctions. Otherwise you may have to recollect the data by
> hand, which is probably not trivial (I have never tried).
>
> I hope what I wrote was not already known to you, goodbye.
> --
> Lorenzo Paulatto
> +39 040 3787 511
> http://people.sissa.it/~paulatto/
>
>
> ----------------------------------------------------------------
> 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
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From paulatto at sissa.it  Thu Dec 13 15:55:06 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Thu, 13 Dec 2007 15:55:06 +0100 (CET)
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
	<8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
	<aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>
Message-ID: <13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it>


On Thu, December 13, 2007 15:06, xu yuehua wrote:
> thank you for your detailed analysis.  your guess is right .my outdir is
> set
> to a place,not local to the nodes.i know the reason of my slow
> job,although
> i did not know it through.
> as for how to use a local directory as outdir ,it seems another new thing
> for me.
> would it be possible to tell me about that ?
> thank you in advance


You let's assume you can write in the /tmp directory on all the nodes
(usually you can) you can use a subdirectory of /tmp as outdir, let's say
/tmp/xy-job

Just set outdir='/tmp/xy-job' in the control namelist. The directory has
to exist on every node.

It is boring to create them by hand you can use ssh with (password-less)
pubkey and some bash cycle, or you can use expect.. you could also try to
use mpirun in some creative way, like
  mpirun -np 8 mkdir -p /tmp/xy-job
but I wouldn't bet on this to work.

I hope this helps
-- 
Lorenzo Paulatto
+39 040 3787 511
http://people.sissa.it/~paulatto/


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


From matteo at umn.edu  Thu Dec 13 16:38:26 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 13 Dec 2007 09:38:26 -0600
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <20071213122653.GA8219@physik.fu-berlin.de>
References: <002201c83d5b$7f75e450$7e61acf0$@net>
	<20071213122653.GA8219@physik.fu-berlin.de>
Message-ID: <8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>



Dear Paul,

I have no experience with CuO and can't give you a very useful  
advise. I suspect that even if you change occ_loc = 9 for Cu the
code will converge to the same ground state. This is however quick to  
try and you may find better results (sometimes the code gets trapped in
local minima with a finite U).

On Dec 13, 2007, at 6:26 AM, Henning Glawe wrote:

> On Wed, Dec 12, 2007 at 11:40:56PM -0800, Paul M. Grant wrote:
>> Simplistically, the initial d-state configuration of Cu2+ in CuO  
>> by Hund?s
>> Rule should be 3d9 (one empty minority spin state state?a hole).    
>> But, with
>> nspin=2, lda_plus_u set true, and U=5 eV (arbitrary), the initial  
>> minority
>> spin occupation gets set to unity, not 4/5 on average (3/5 for Ni  
>> and 1/5
>> for Fe).  Is this due to occ_loc being set to 10 in tabd.f90 and  
>> not 9 (it?s
>> 6 for Fe and 8 for Ni)?  The occupation distribution converges to  
>> around
>
> as the d shell can be filled with 10 electrons, getting a initial  
> hole into the
> d shell while occ_loc=10 is IMHO impossible.
>
>
>> functionals have equivalent occupations and give similar  
>> results).  When I
>> try Cu.pz-d-rrkjus.UPF, with 3d10, 4s1 and 4p-1(!!!), the first scf
>> iteration yields individual spin occupations of nearly 5(!!!), and  
>> the
>> situation gets really ugly thereafter.
>
> I also encountered this problem with this pseudo potential; the  
> problem lies
> in the normalization of the 3d wave functions saved in the pp file.  
> if you
> search in the archives of the pw forum, you will find a patch for  
> pwscf
> allowing to recalculate the norm of the atomic states after the pp  
> file has
> been read.
>


the patch has been implemented in the cvs version of the code. if you  
download it and read INPUT_PW
you find the following lines (you are interested in norm-atomic):


U_projection_type   CHARACTER   (default='atomic')
                Only active when lda_plus_U is .true., specifies the  
type
                of projector on localized orbital to be used in the  
LDA+U
                scheme.
                Currently available choices:
                'atomic': use atomic wfc's (as they are) to build the  
projector
                'ortho-atomic': use Lowdin orthogonalized atomic wfc's
                'norm-atomic': Lowdin normalization of atomic wfc.  
Keep in mind:
                               atomic wfc are not orthogonalized in  
this case.
                               This is a "quick and dirty" trick to  
be used when
                               atomic wfc from the pseudopotential  
are not
                               normalized (and thus produce  
occupation whose
                               value exceeds unity). If  
orthogonalized wfc are
                               not needed always try 'atomic' first.
                'file': use the information from file "prefix".atwfc  
that must
                        have been generated previously, for instance  
by pmw.x
                        (see PP/poormanwannier.f90 for details)
                NB: forces and stress currently implemented only for the
                    'atomic' choice.


Hope this helps.

Matteo


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

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From baroni at sissa.it  Thu Dec 13 16:47:50 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Thu, 13 Dec 2007 15:47:50 +0000
Subject: [Pw_forum] IFC's and eigendisplacements in example06
In-Reply-To: <75810c7f0712122354o3de01076t3168b04777e92734@mail.gmail.com>
References: <75810c7f0712122354o3de01076t3168b04777e92734@mail.gmail.com>
Message-ID: <B907DDA7-4A0D-48AA-BF51-FBD140508EFE@sissa.it>

Dear ?mer:

> 1) Could you give me some analysis and explanations on the range of  
> the interatomic force constants (IFC's) for AlAs in example06.
>  On the Forum, there are  some informations and explanations but i  
> don't understand them. I need more explanations.

ask a question and we will try to answer. "give me some explanations"  
is not a question. We could give many explanations to problems that  
you do not have, so we would waste my time. In the lack of any hints  
on what your problem is, the best advice I can give you is to study  
some classical textbooks on lattice dynamics (such as Born and Huang)

>  2) Is there a meaning of ratio of displacement of the two ions (Al  
> and As) in the eigendisplacement pattern?

the meaning is that they are normal modes in the sense that is  
explained in the "small vibrations" chapter of any classical mechanics  
textbook (such as, e.g. Landau or Goldstein)

> The calculated vibrational eigenvectors at X point are below. How  
> can we evaluate this data?

what do you want to evaluate?

SB
>

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

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



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From w2agz at pacbell.net  Thu Dec 13 19:41:47 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Thu, 13 Dec 2007 10:41:47 -0800
Subject: [Pw_forum] bands_FS.x and spin polarized metals
In-Reply-To: <11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it>
References: <000001c83cfe$26acd5c0$74068140$@net>
	<11D38E47-D9DB-4F1A-B8BC-58E56B1455DF@nest.sns.it>
Message-ID: <00a001c83db7$d12d5e20$73881a60$@net>

Paolo, I'm sure I'm older than you!

You're absolutely right.  Abend was coined by the designers of the IBM 701.
Mean time to failure on the early prototypes of that machine was only about
three hours.

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


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Paolo Giannozzi
Sent: Wednesday, December 12, 2007 12:50 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] bands_FS.x and spin polarized metals


On Dec 12, 2007, at 21:32 , Paul M. Grant wrote:

> And sure enough, if you?re dumb and try anyway, it abends with a  
> read error
>

I am old enough to have seen card punchers in action, so the term
"abend" is not unknown to me, but I guess younger people don't
know that it is a shorthand for "abnormal end", on IBM mainframes...

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 amigliore at cmm.upenn.edu  Thu Dec 13 23:24:57 2007
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Thu, 13 Dec 2007 17:24:57 -0500 (EST)
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>
	<20071213122653.GA8219@physik.fu-berlin.de>
	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>
Message-ID: <3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>

Hello

Also independently of this specific problem, I use the occasion to say
that sometimes, with finite U, the code gets trapped in local minima for
some values of the "mixing_beta" parameter.

Agostino Migliore


From amigliore at cmm.upenn.edu  Thu Dec 13 23:27:00 2007
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Thu, 13 Dec 2007 17:27:00 -0500 (EST)
Subject: [Pw_forum] Local density of electronic entropy
In-Reply-To: <0D28E239-B6EF-4814-9892-A612822DEB2D@nest.sns.it>
References: <b8b82da20712100252xc2e938aka6829ce95a9c44d3@mail.gmail.com>
	<0D28E239-B6EF-4814-9892-A612822DEB2D@nest.sns.it>
Message-ID: <3090.130.91.67.162.1197584820.squirrel@cmm.upenn.edu>

Hello

Some useful equations (directly matching your need or providing good
grounds) can be found on Phys. Rev. B 58, 13459 (1998) and other
papers by F?hnle.

Agostino Migliore

>
> On Dec 10, 2007, at 11:52 , Clark Lee wrote:
>
>> I am very appreciated getting some literature or theoretical
>> background
>> about 'local density of electronic entropy'.


From amigliore at cmm.upenn.edu  Thu Dec 13 23:04:14 2007
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Thu, 13 Dec 2007 17:04:14 -0500 (EST)
Subject: [Pw_forum] Local density of electronic entropy
In-Reply-To: <0D28E239-B6EF-4814-9892-A612822DEB2D@nest.sns.it>
References: <b8b82da20712100252xc2e938aka6829ce95a9c44d3@mail.gmail.com>
	<0D28E239-B6EF-4814-9892-A612822DEB2D@nest.sns.it>
Message-ID: <2677.130.91.67.162.1197583454.squirrel@cmm.upenn.edu>

Hello

Some useful equations (directly matching your need or providing good
grounds) can be found on Phys. Rev. B 58, 13459 (1998) and other
papers by F?hnle.

Agostino Migliore

>
> On Dec 10, 2007, at 11:52 , Clark Lee wrote:
>
> I am very appreciated getting some literature or theoretical
> background
> about 'local density of electronic entropy'.


From matteo at umn.edu  Fri Dec 14 00:23:07 2007
From: matteo at umn.edu (Matteo Cococcioni)
Date: Thu, 13 Dec 2007 17:23:07 -0600
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>
	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>
Message-ID: <4761BEDB.8020501@umn.edu>


Hi Agostino

what kind of system are you referring to? it must be one with several 
minima. if this is the case I think you get to a different one changing 
whatever parameter in the input just because of (slightly) different 
initial conditions or numerical noise that may bias the system towards a 
different state. I'm not sure what could be a good way to explore them 
all or to bias the system towards the "right" (lowest energy) one. Maybe 
using fractals..... (just kidding). Seriously, if one can distinguish 
the minima then one can write a constraint but what is a relevant degree 
of freedom to perturb in general?

Thinking of CuO I have the suspect that in this system the hybridization 
between Cu and O is important (although the electron may still be quite 
localized). If this is the case then the lda+U on atomic orbitals may be 
not a good idea because it will force integer occupations on atomic orbitals
while hybridization requires sharing of electrons between different 
atoms. Probably wannier functions (that Paul was going to try) are a 
better option.

Matteo



Agostino Migliore wrote:
> Hello
>
> Also independently of this specific problem, I use the occasion to say
> that sometimes, with finite U, the code gets trapped in local minima for
> some values of the "mixing_beta" parameter.
>
> Agostino Migliore
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   

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From amigliore at cmm.upenn.edu  Fri Dec 14 00:42:15 2007
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Thu, 13 Dec 2007 18:42:15 -0500 (EST)
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <4761BEDB.8020501@umn.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>
	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>
	<4761BEDB.8020501@umn.edu>
Message-ID: <3645.130.91.67.162.1197589335.squirrel@cmm.upenn.edu>

Hello

I refer to cations in solution (e.g., Fe2+/Fe3+). Indeed, I explored all
parameters and concluded that "the" minimum can be safely found. The only
problem is that for some configuration of the system and some particular
value of the mixing_beta parameter the calculation ends on a local
minimum. In these (indeed infrequent) cases, anyway the (same) minimum is
gotten along a wide range of the mixing_beta parameter, while a higher
minimum (e.g., the energy is 0.01 Ry more, which is significant for my
work) is reached at a particular mixing_beta value.
Let me express my agreement for the consideration about hybridization, on
which I reflected between this email and the previous one.

Agostino

>
> Hi Agostino
>
> what kind of system are you referring to? it must be one with several
> minima. if this is the case I think you get to a different one changing
> whatever parameter in the input just because of (slightly) different
> initial conditions or numerical noise that may bias the system towards a
> different state. I'm not sure what could be a good way to explore them
> all or to bias the system towards the "right" (lowest energy) one. Maybe
> using fractals..... (just kidding). Seriously, if one can distinguish
> the minima then one can write a constraint but what is a relevant degree
> of freedom to perturb in general?
>
> Thinking of CuO I have the suspect that in this system the hybridization
> between Cu and O is important (although the electron may still be quite
> localized). If this is the case then the lda+U on atomic orbitals may be
> not a good idea because it will force integer occupations on atomic
> orbitals
> while hybridization requires sharing of electrons between different
> atoms. Probably wannier functions (that Paul was going to try) are a
> better option.
>
> Matteo
>
>
>


From marzari at MIT.EDU  Fri Dec 14 04:17:34 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 13 Dec 2007 22:17:34 -0500
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>
	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>
Message-ID: <4761F5CE.8030807@mit.edu>

Agostino Migliore wrote:
> Hello
> 
> Also independently of this specific problem, I use the occasion to say
> that sometimes, with finite U, the code gets trapped in local minima for
> some values of the "mixing_beta" parameter.

Did you characterize the local minimum, by any chance ? The system
is fairly simple (on one side, 5 d electrons, say all up, and
on the other side, 6 d electrons). Do you have a sense if the
additional minimum is due to some long range ferro vs. antiferro
coupling between the two ions (i.e. 5 up on one side, and 5 up and
1 down, vs 5 up, 5 down and 1 up), or if the minorit spin on the ferric
ion splits in two or three orbtials with fractional occupations ?


			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 amigliore at cmm.upenn.edu  Fri Dec 14 06:32:51 2007
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Fri, 14 Dec 2007 00:32:51 -0500 (EST)
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <4761F5CE.8030807@mit.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>
	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>
	<4761F5CE.8030807@mit.edu>
Message-ID: <2522.130.91.67.162.1197610371.squirrel@cmm.upenn.edu>

I noted that one of my previous emails was misleading. In fact, the system
is Fe2+/Fe3+, but I noticed the problem when performing calculations on a
single solvated ion, with Fe2+ and no fractional occupations. The system
can anyway get a local minimum for some configuration and some mixing_beta
value (let me remark that this occurs rarely), and this can happen both
with a constrained total magnetization and without it. It seems just a
convergence problem connected to the mixing factor.

Hello
Agostino

> Agostino Migliore wrote:
>> Hello
>>
>> Also independently of this specific problem, I use the occasion to say
>> that sometimes, with finite U, the code gets trapped in local minima for
>> some values of the "mixing_beta" parameter.
>
> Did you characterize the local minimum, by any chance ? The system
> is fairly simple (on one side, 5 d electrons, say all up, and
> on the other side, 6 d electrons). Do you have a sense if the
> additional minimum is due to some long range ferro vs. antiferro
> coupling between the two ions (i.e. 5 up on one side, and 5 up and
> 1 down, vs 5 up, 5 down and 1 up), or if the minorit spin on the ferric
> ion splits in two or three orbtials with fractional occupations ?
>
>
> 			nicola


From marzari at MIT.EDU  Fri Dec 14 06:42:32 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 14 Dec 2007 00:42:32 -0500
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <2522.130.91.67.162.1197610371.squirrel@cmm.upenn.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>	<4761F5CE.8030807@mit.edu>
	<2522.130.91.67.162.1197610371.squirrel@cmm.upenn.edu>
Message-ID: <476217C8.70806@mit.edu>



Dear Agostino,

if the calculation did converge to a local minimum, it means that the
system has more than one minimum, not that there is a convergence
problem (of course, the convergence strategy you choose will affect
the minimum in which you fall).

It would be very interesting to know more (when you have time) about
these minima - e.g. what were the projections of the minority spin
in the two cases.

Thanks !

			nicola


Agostino Migliore wrote:
> I noted that one of my previous emails was misleading. In fact, the system
> is Fe2+/Fe3+, but I noticed the problem when performing calculations on a
> single solvated ion, with Fe2+ and no fractional occupations. The system
> can anyway get a local minimum for some configuration and some mixing_beta
> value (let me remark that this occurs rarely), and this can happen both
> with a constrained total magnetization and without it. It seems just a
> convergence problem connected to the mixing factor.
> 
> Hello
> Agostino

---------------------------------------------------------------------
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 amigliore at cmm.upenn.edu  Fri Dec 14 07:00:43 2007
From: amigliore at cmm.upenn.edu (Agostino Migliore)
Date: Fri, 14 Dec 2007 01:00:43 -0500 (EST)
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <476217C8.70806@mit.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>	<4761F5CE.8030807@mit.edu>
	<2522.130.91.67.162.1197610371.squirrel@cmm.upenn.edu>
	<476217C8.70806@mit.edu>
Message-ID: <2741.130.91.67.162.1197612043.squirrel@cmm.upenn.edu>

Yes, I know. By saying "convergence problem" I just meant, in this
specific case, that the scf calculation does not reach the right minimum
(i.e., the lowest one), but get trapped into some another (local) minimum.
As to your second point, I will send you a further email in a short time.
Thank you

Agostino
>
>
> Dear Agostino,
>
> if the calculation did converge to a local minimum, it means that the
> system has more than one minimum, not that there is a convergence
> problem (of course, the convergence strategy you choose will affect
> the minimum in which you fall).
>
> It would be very interesting to know more (when you have time) about
> these minima - e.g. what were the projections of the minority spin
> in the two cases.
>
> Thanks !
>
> 			nicola


From w2agz at pacbell.net  Fri Dec 14 08:20:27 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Thu, 13 Dec 2007 23:20:27 -0800
Subject: [Pw_forum] CuO, LDA+U, Pseudopots, etc.
In-Reply-To: <2741.130.91.67.162.1197612043.squirrel@cmm.upenn.edu>
References: <002201c83d5b$7f75e450$7e61acf0$@net>	<20071213122653.GA8219@physik.fu-berlin.de>	<8821E722-1F25-484E-8E7A-F3E906A96651@umn.edu>	<3061.130.91.67.162.1197584697.squirrel@cmm.upenn.edu>	<4761F5CE.8030807@mit.edu>	<2522.130.91.67.162.1197610371.squirrel@cmm.upenn.edu>	<476217C8.70806@mit.edu>
	<2741.130.91.67.162.1197612043.squirrel@cmm.upenn.edu>
Message-ID: <00d001c83e21$cdf99d30$69ecd790$@net>

To All responding to my initial thread:

I'm amazed and encouraged by the response of the community to my problem.  I
will be trying your suggestions...e.g., a "rich man's" Wannier projection.
Of course, this trapping into a "metastable state" is typical of many highly
nonlinear systems of any type...such as the many body nonlinear
Navier-Stokes equations, sometimes referred to as the "weather."

Someone pointed out the importance of covalency in the Cu-O double bond, and
I'm not sure how to accommodate this in PWscf (in the simple Hubbard
Hamiltonian, you just futz around with U and t in a Monte Carlo
simulation...in 1 or 2 dimensions).  As I mentioned in my original posting,
there may be a profound issue here that DFT LDA+U may find difficult to
address...it's probably the origin of HTSC.  There is a polemic published
back in 1989 by Phil Anderson to the effect that pseudopotential theory may
not apply to divalent Cu-O bonds.

Nonetheless, I would still like to find a way to get a Hubbard Gap in
divalent CuO from a PW/PP starting point.  I'm old enough to remember this
was once quite a task for NiO.

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


-----Original Message-----
From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of Agostino Migliore
Sent: Thursday, December 13, 2007 10:01 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] CuO, LDA+U, Pseudopots, etc.

Yes, I know. By saying "convergence problem" I just meant, in this
specific case, that the scf calculation does not reach the right minimum
(i.e., the lowest one), but get trapped into some another (local) minimum.
As to your second point, I will send you a further email in a short time.
Thank you

Agostino
>
>
> Dear Agostino,
>
> if the calculation did converge to a local minimum, it means that the
> system has more than one minimum, not that there is a convergence
> problem (of course, the convergence strategy you choose will affect
> the minimum in which you fall).
>
> It would be very interesting to know more (when you have time) about
> these minima - e.g. what were the projections of the minority spin
> in the two cases.
>
> Thanks !
>
> 			nicola

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


From njuxuyuehua at gmail.com  Fri Dec 14 09:09:30 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 14 Dec 2007 16:09:30 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
	<8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
	<aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>
	<13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it>
Message-ID: <aca2feb20712140009i73cb322awef7b0979b863f387@mail.gmail.com>

thank you .although it does not work

2007/12/13, Lorenzo Paulatto <paulatto at sissa.it>:
>
>
> On Thu, December 13, 2007 15:06, xu yuehua wrote:
> > thank you for your detailed analysis.  your guess is right .my outdir is
> > set
> > to a place,not local to the nodes.i know the reason of my slow
> > job,although
> > i did not know it through.
> > as for how to use a local directory as outdir ,it seems another new
> thing
> > for me.
> > would it be possible to tell me about that ?
> > thank you in advance
>
>
> You let's assume you can write in the /tmp directory on all the nodes
> (usually you can) you can use a subdirectory of /tmp as outdir, let's say
> /tmp/xy-job
>
> Just set outdir='/tmp/xy-job' in the control namelist. The directory has
> to exist on every node.
>
> It is boring to create them by hand you can use ssh with (password-less)
> pubkey and some bash cycle, or you can use expect.. you could also try to
> use mpirun in some creative way, like
> mpirun -np 8 mkdir -p /tmp/xy-job
> but I wouldn't bet on this to work.
>
> I hope this helps
> --
> Lorenzo Paulatto
> +39 040 3787 511
> http://people.sissa.it/~paulatto/
>
>
> ----------------------------------------------------------------
> 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
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From giannozz at nest.sns.it  Fri Dec 14 09:12:20 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 14 Dec 2007 09:12:20 +0100
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <aca2feb20712140009i73cb322awef7b0979b863f387@mail.gmail.com>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
	<8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
	<aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>
	<13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it>
	<aca2feb20712140009i73cb322awef7b0979b863f387@mail.gmail.com>
Message-ID: <D06D625B-93EA-442E-B0F7-4FF5A391B850@nest.sns.it>


On Dec 14, 2007, at 9:09 , xu yuehua wrote:

> thank you .although it does not work

what "does not work", and what do you mean by
"does not work"?
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From njuxuyuehua at gmail.com  Fri Dec 14 09:36:58 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 14 Dec 2007 16:36:58 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <D06D625B-93EA-442E-B0F7-4FF5A391B850@nest.sns.it>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
	<8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
	<aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>
	<13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it>
	<aca2feb20712140009i73cb322awef7b0979b863f387@mail.gmail.com>
	<D06D625B-93EA-442E-B0F7-4FF5A391B850@nest.sns.it>
Message-ID: <aca2feb20712140036k2a1b616av200056de521ed04f@mail.gmail.com>

sorry, in fact ,"want" is  mpirun -np 8 mkdir -p /tmp/xy-job .and the error
message :
Warning: Command line arguments for program should be given
after the program name.  Assuming that -p is a
command line argument for the program.
Warning: Command line arguments for program should be given
after the program name.  Assuming that /tmp/xy-job is a
command line argument for the program.
Missing: program name
Program mkdir either does not exist, is not
executable, or is an erroneous argument to mpirun.




2007/12/14, Paolo Giannozzi <giannozz at nest.sns.it>:
>
>
> On Dec 14, 2007, at 9:09 , xu yuehua wrote:
>
> > thank you .although it does not work
>
> what "does not work", and what do you mean by
> "does not work"?
> ---
> 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
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From hqzhou at nju.edu.cn  Fri Dec 14 10:45:49 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 14 Dec 2007 17:45:49 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com><2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it><aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com><8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it><aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com><13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it><aca2feb20712140009i73cb322awef7b0979b863f387@mail.gmail.com><D06D625B-93EA-442E-B0F7-4FF5A391B850@nest.sns.it>
	<aca2feb20712140036k2a1b616av200056de521ed04f@mail.gmail.com>
Message-ID: <01ea01c83e36$1bfed220$1d00a8c0@solarflare>

Yuehua,

You don't need to issue mpirun command that way, just to point outdir
to a local directory, say /tmp/your_job, as Lorenzo suggested, but note
you must have read/write permission for the directory.

If you belong to the condensed matter physics group of Nanjing University,
the cluster you are using should be built using ROCKS. Then, everything is
easy, just run

$ cluster-fork mkdir /state/partition1/yuehua 

This command will create a folder on every compute nodes.
then, set "outdir = /state/partition1/yuehua/" in your input file.


Huiqun Zhou
@Earth Sciences, Nanjing University, China

  ----- Original Message ----- 
  From: xu yuehua 
  To: PWSCF Forum 
  Sent: Friday, December 14, 2007 4:36 PM
  Subject: Re: [Pw_forum] how to control the writing of wavefunction


  sorry, in fact ,"want" is  mpirun -np 8 mkdir -p /tmp/xy-job .and the error message :
  Warning: Command line arguments for program should be given
  after the program name.  Assuming that -p is a
  command line argument for the program.
  Warning: Command line arguments for program should be given
  after the program name.  Assuming that /tmp/xy-job is a
  command line argument for the program.
  Missing: program name
  Program mkdir either does not exist, is not 
  executable, or is an erroneous argument to mpirun. 



   
  2007/12/14, Paolo Giannozzi <giannozz at nest.sns.it>: 

    On Dec 14, 2007, at 9:09 , xu yuehua wrote:

    > thank you .although it does not work

    what "does not work", and what do you mean by 
    "does not work"?
    ---
    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




  -- 
  Xu Yuehua
  physics Department of Nanjing university
  China 


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


  _______________________________________________
  Pw_forum mailing list
  Pw_forum at pwscf.org
  http://www.democritos.it/mailman/listinfo/pw_forum
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From chen_shao_hua197 at yahoo.com.tw  Fri Dec 14 13:24:47 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Fri, 14 Dec 2007 20:24:47 +0800 (CST)
Subject: [Pw_forum] Could PWscf code handle the atom or molecule in external
	magnetic field ?
Message-ID: <480522.74293.qm@web73008.mail.tp2.yahoo.com>

Dear forum's members,

I wonder could PWscf code handle the atom or molecule
in external magnetic field ?
If can, how to setting external magnetic field ?
Thanks in advance

max
Physics department, National Taiwan University, Taiwan


      ______________________________________________________________________________________
??????????????????????????????http://tw.promo.yahoo.com/antispam/index.html

From jkiitb at gmail.com  Fri Dec 14 13:57:03 2007
From: jkiitb at gmail.com (jitendra mishra)
Date: Fri, 14 Dec 2007 18:27:03 +0530
Subject: [Pw_forum] Electron-phonon calculation
Message-ID: <a212af800712140457r615a2e6cge37e60e828cf2e93@mail.gmail.com>

Dear Sir,
While calculating electron-phonon calculation I'm getting
matdyn.out.dosfile in which it is written that Z* not found in TO-LO
splitting.
Please tell me what is the problem.


Thanks & Regards,

-- 
JITENDRA KUMAR MISHRA
Room no:-B-701, H-13, IIT BOMBAY,POWAI,
MUMBAI-400076
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From giannozz at nest.sns.it  Fri Dec 14 14:02:40 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 14 Dec 2007 14:02:40 +0100
Subject: [Pw_forum] Electron-phonon calculation
In-Reply-To: <a212af800712140457r615a2e6cge37e60e828cf2e93@mail.gmail.com>
References: <a212af800712140457r615a2e6cge37e60e828cf2e93@mail.gmail.com>
Message-ID: <B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>


On Dec 14, 2007, at 13:57 , jitendra mishra wrote:

> While calculating electron-phonon calculation
> I'm getting matdyn.out.dos file in which it is written
> that Z* not found in TO-LO splitting.

Z* are not calculated in metals

> Please tell me what is the problem

there is no problem at all
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From njuxuyuehua at gmail.com  Fri Dec 14 15:00:00 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 14 Dec 2007 22:00:00 +0800
Subject: [Pw_forum] how to control the writing of wavefunction
In-Reply-To: <01ea01c83e36$1bfed220$1d00a8c0@solarflare>
References: <aca2feb20712130006y165e92e2rc4ebc72694f825c0@mail.gmail.com>
	<2948.147.122.5.182.1197541562.squirrel@webmail.sissa.it>
	<aca2feb20712130442t785f6b35sdda08aafed5cc587@mail.gmail.com>
	<8414.147.122.5.182.1197551761.squirrel@webmail.sissa.it>
	<aca2feb20712130606l792da093n6e040015a2d23fc@mail.gmail.com>
	<13083.147.122.5.182.1197557706.squirrel@webmail.sissa.it>
	<aca2feb20712140009i73cb322awef7b0979b863f387@mail.gmail.com>
	<D06D625B-93EA-442E-B0F7-4FF5A391B850@nest.sns.it>
	<aca2feb20712140036k2a1b616av200056de521ed04f@mail.gmail.com>
	<01ea01c83e36$1bfed220$1d00a8c0@solarflare>
Message-ID: <aca2feb20712140559i24a31183o77f1f952c0d9b9ee@mail.gmail.com>

thank you ,it does work now.
 bests
                              xuyuehua

2007/12/14, Huiqun Zhou <hqzhou at nju.edu.cn>:
>
>  Yuehua,
>
> You don't need to issue mpirun command that way, just to point outdir
> to a local directory, say /tmp/your_job, as Lorenzo suggested, but note
> you must have read/write permission for the directory.
>
> If you belong to the condensed matter physics group of Nanjing University,
> the cluster you are using should be built using ROCKS. Then, everything is
> easy, just run
>
> $ cluster-fork mkdir /state/partition1/yuehua
>
> This command will create a folder on every compute nodes.
> then, set "outdir = /state/partition1/yuehua/" in your input file.
>
>
> Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
>
>  ----- Original Message -----
> *From:* xu yuehua <njuxuyuehua at gmail.com>
> *To:* PWSCF Forum <pw_forum at pwscf.org>
> *Sent:* Friday, December 14, 2007 4:36 PM
> *Subject:* Re: [Pw_forum] how to control the writing of wavefunction
>
>
> sorry, in fact ,"want" is  mpirun -np 8 mkdir -p /tmp/xy-job .and the
> error message :
> Warning: Command line arguments for program should be given
> after the program name.  Assuming that -p is a
> command line argument for the program.
> Warning: Command line arguments for program should be given
> after the program name.  Assuming that /tmp/xy-job is a
> command line argument for the program.
> Missing: program name
> Program mkdir either does not exist, is not
> executable, or is an erroneous argument to mpirun.
>
>
>
>
> 2007/12/14, Paolo Giannozzi <giannozz at nest.sns.it>:
> >
> >
> > On Dec 14, 2007, at 9:09 , xu yuehua wrote:
> >
> > > thank you .although it does not work
> >
> > what "does not work", and what do you mean by
> > "does not work"?
> > ---
> > 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
> >
>
>
>
> --
> Xu Yuehua
> physics Department of Nanjing university
> China
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Xu Yuehua
physics Department of Nanjing university
China
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From sks.jnc at gmail.com  Fri Dec 14 18:15:42 2007
From: sks.jnc at gmail.com (S. K. S.)
Date: Fri, 14 Dec 2007 22:45:42 +0530
Subject: [Pw_forum] Vanderbilt USPP
Message-ID: <d5eefb3d0712140915m21106e08s22b3d54c8d8d97b6@mail.gmail.com>

 Dear Users,

 Can anyone please tell me whether  the Vanderbilt USPP for
 Bi,   Sm,  Gd and Dy  are available or not ?

 Regards,

  SKS
  PhD
 Jncasr
  India
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From degironc at sissa.it  Fri Dec 14 18:25:38 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Fri, 14 Dec 2007 18:25:38 +0100
Subject: [Pw_forum] Vanderbilt USPP
In-Reply-To: <d5eefb3d0712140915m21106e08s22b3d54c8d8d97b6@mail.gmail.com>
References: <d5eefb3d0712140915m21106e08s22b3d54c8d8d97b6@mail.gmail.com>
Message-ID: <4762BC92.6080902@sissa.it>

S. K. S. wrote:
>
>
>  Dear Users,
>
>  Can anyone please tell me whether  the Vanderbilt USPP for
>  Bi,   Sm,   Gd and  Dy  are available or not ? 
to my knowledge: yes, no,no,no
for Bi pseudo check http://www.pwscf.net/pseudo/1.3/html/Bi.html or 
http://www.physics.rutgers.edu/~dhv/uspp/index.html#LIBRARY

Stefano de Gironcoli -SISSA and DEMOCRITOS
>
>
>  Regards,
>
>   SKS
>   PhD
>  Jncasr
>   India
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From mmarques at staffmail.ed.ac.uk  Fri Dec 14 20:18:37 2007
From: mmarques at staffmail.ed.ac.uk (Miriam Marques)
Date: Fri, 14 Dec 2007 19:18:37 +0000
Subject: [Pw_forum] Raman and IR intensities for a metal
Message-ID: <20071214191837.ezu180ga8sgkcs40@www.staffmail.ed.ac.uk>

  Dear ESPRESSO users,

  I would like to know if it is possible to compute
  Raman and Infrared intensities for a metallic system.

  Thank you very much in advance,

  Miriam.

  Dr. Miriam Marques
  Centre for Science at Extreme Conditions.
  The University of Edinburgh.
  e-mail: mmarques at staffmail.ed.ac.uk


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



From baroni at sissa.it  Fri Dec 14 22:31:26 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 14 Dec 2007 21:31:26 +0000
Subject: [Pw_forum] Electron-phonon calculation
In-Reply-To: <B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>
References: <a212af800712140457r615a2e6cge37e60e828cf2e93@mail.gmail.com>
	<B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>
Message-ID: <38F1C217-4A4E-4E34-A86B-A42532AC3CB8@sissa.it>


On Dec 14, 2007, at 1:02 PM, Paolo Giannozzi wrote:

>
> On Dec 14, 2007, at 13:57 , jitendra mishra wrote:
>
>> While calculating electron-phonon calculation
>> I'm getting matdyn.out.dos file in which it is written
>> that Z* not found in TO-LO splitting.
>
> Z* are not calculated in metals

even more: z*=0 in metals (that's why they are not calculated)

SB

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

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



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From baroni at sissa.it  Fri Dec 14 22:41:54 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 14 Dec 2007 21:41:54 +0000
Subject: [Pw_forum] Electron-phonon calculation
In-Reply-To: <B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>
References: <a212af800712140457r615a2e6cge37e60e828cf2e93@mail.gmail.com>
	<B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>
Message-ID: <1E53CAA5-63BF-4FCF-B976-F6C677851431@sissa.it>


On Dec 14, 2007, at 1:02 PM, Paolo Giannozzi wrote:

>
> On Dec 14, 2007, at 13:57 , jitendra mishra wrote:
>
>> While calculating electron-phonon calculation
>> I'm getting matdyn.out.dos file in which it is written
>> that Z* not found in TO-LO splitting.
>
> Z* are not calculated in metals

even more: z*=0 in metals (that's why they are not calculated)

SB

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

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



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From baroni at sissa.it  Fri Dec 14 22:31:26 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 14 Dec 2007 21:31:26 +0000
Subject: [Pw_forum] Electron-phonon calculation
In-Reply-To: <B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>
References: <a212af800712140457r615a2e6cge37e60e828cf2e93@mail.gmail.com>
	<B3708FD7-11F1-4325-A6D7-9D558FB75036@nest.sns.it>
Message-ID: <38F1C217-4A4E-4E34-A86B-A42532AC3CB8@sissa.it>


On Dec 14, 2007, at 1:02 PM, Paolo Giannozzi wrote:

>
> On Dec 14, 2007, at 13:57 , jitendra mishra wrote:
>
>> While calculating electron-phonon calculation
>> I'm getting matdyn.out.dos file in which it is written
>> that Z* not found in TO-LO splitting.
>
> Z* are not calculated in metals

even more: z*=0 in metals (that's why they are not calculated)

SB

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

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



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From baroni at sissa.it  Fri Dec 14 22:46:52 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 14 Dec 2007 21:46:52 +0000
Subject: [Pw_forum] Raman and IR intensities for a metal
In-Reply-To: <20071214191837.ezu180ga8sgkcs40@www.staffmail.ed.ac.uk>
References: <20071214191837.ezu180ga8sgkcs40@www.staffmail.ed.ac.uk>
Message-ID: <043BD905-AA7A-42B3-8E7F-FA9497DF3E4C@sissa.it>

Dear Miriam: you and others will forgive my ignorance, but I would  
need some further explanations. According to the usual theory, they  
both should be zero:````````````````````` the second is given by Born  
effective charges (that are zero in metals), the former by the  
derivative of the inverse macroscopic electric constant (which is also  
zero). How can a metal be Raman or IR active? Thanks - SB

On Dec 14, 2007, at 7:18 PM, Miriam Marques wrote:

>  Dear ESPRESSO users,
>
>  I would like to know if it is possible to compute
>  Raman and Infrared intensities for a metallic system.
>
>  Thank you very much in advance,
>
>  Miriam.
>
>  Dr. Miriam Marques
>  Centre for Science at Extreme Conditions.
>  The University of Edinburgh.
>  e-mail: mmarques at staffmail.ed.ac.uk
>
>
> -- 
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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



-------------- next part --------------
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From oulihui666 at 126.com  Sat Dec 15 02:49:35 2007
From: oulihui666 at 126.com (oulihui666)
Date: Sat, 15 Dec 2007 09:49:35 +0800 (CST)
Subject: [Pw_forum] Question about pdos
Message-ID: <3958189.69651197683375764.JavaMail.coremail@bj126app81.126.com>

Dear pwscf users,
   I have a question, quite naive. I tried to search the pdos of oxygen molecular, but I have to rely on your advice. as well as I know,the calculation procedes as follows:
1) make a self-consistent calculation (input=O2.scf.in)
2) run a non-self-consistent calculation (input=O2.nscf.in)
3) run projwfc.x program (input=O2.pdos.in, output=O2.pdos.out)in order to produce a postscript file: O2.pdos_tot.
    After scf and nscf calculation, the program pdos was used as follows:
 &INPUTPP
                      prefix = 'O2' ,
                      outdir = '/home/olh/tmp/' ,
                     filpdos = 'O2.pdos',
                      ngauss = 1,
                     degauss = 0.02,
                      DeltaE = 0.01 ,
                        Emin = -35 ,
                        Emax = -4 ,
 /
    However, when I calculated pdos, in order to produce a postscript file: O2.pdos_tot, I encounter a problem, output is displayed as follows:
.....
k =  -0.3750000000 -0.2165063509  0.1678415576
     e =   -30.88771 eV
     psi = 
    |psi|^2 =   NaN
     e =   -18.42806 eV
     psi = 
    |psi|^2 =   NaN
     e =   -12.12292 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.97042 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.96565 eV
     psi = 
    |psi|^2 =   NaN
     e =    -4.27073 eV
     psi = 
    |psi|^2 =   NaN
 k =   0.0000000000 -0.4330127019 -0.1678415576
     e =   -30.88770 eV
     psi = 
    |psi|^2 =   NaN
     e =   -18.42864 eV
     psi = 
    |psi|^2 =   NaN
     e =   -12.12059 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.96946 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.96552 eV
     psi = 
    |psi|^2 =   NaN
     e =    -4.27538 eV
     psi = 
    |psi|^2 =   NaN
Lowdin Charges: 
     Atom #   1: total charge =      NaN, s, p, d, f =      NaN     NaN
                 spin up      =      NaN, s, p, d, f =      NaN     NaN
                 spin down    =      NaN, s, p, d, f =      NaN     NaN
                 polarization =      NaN, s, p, d, f =      NaN     NaN
     Atom #   2: total charge =      NaN, s, p, d, f =      NaN     NaN
                 spin up      =      NaN, s, p, d, f =      NaN     NaN
                 spin down    =      NaN, s, p, d, f =      NaN     NaN
                 polarization =      NaN, s, p, d, f =      NaN     NaN
     Spilling Parameter:      NaN
It displayed "NaN", not numerical, I am confused.
Any suggestions is appreciated.
 
Thank you in advance
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 yupiaofei at mail.sdu.edu.cn  Sat Dec 15 04:44:57 2007
From: yupiaofei at mail.sdu.edu.cn (yupiaofei(SDU))
Date: Sat, 15 Dec 2007 11:44:57 +0800
Subject: [Pw_forum] Optical properties
References: <397513651.07592@mail.sdu.edu.cn> <397533402.31255@mail.sdu.edu.cn>
Message-ID: <397690649.25502@mail.sdu.edu.cn>

Dear Andrea,

According to your guidance, I compiled the epsilon.x successfully, but I have two questions,

i.  I tested the epsilon.x, and it could read the outputfile by PWSCF3.2. However, it can't read the save file by 
PW3.0. Is that true?

ii. The epsilon.x cann't support the ultra soft PP?


sincerely

Kesong Yang

School of Physics and Microelectronics

Shandong University, Jinan 250100, People's Republic of China

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From njuxuyuehua at gmail.com  Sat Dec 15 14:17:19 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Sat, 15 Dec 2007 21:17:19 +0800
Subject: [Pw_forum] help : E VS C curve gets worse whne i enlarge encut and
	ecutrho
In-Reply-To: <aca2feb20712150131i6bb027eblec959fce8453b416@mail.gmail.com>
References: <aca2feb20712150131i6bb027eblec959fce8453b416@mail.gmail.com>
Message-ID: <aca2feb20712150517q91c4f45s71cfb47791cbdcb3@mail.gmail.com>

hi all:
i am writing to ask  all if it is possible  to give me some advice about my
strange problem.
i relaxed only one crystall lattice c ,and get   E Vs C ,someone kindly
enough to suggest me to enlarge the encut and ecutetho in order to get
smoother parabola.but things go contrary to my wishes,the curve gets worse
,it is serration.
i enclose  the curve. the first graph is encut ,40,ecutrho 400,and the last
is 35,350. (uspp)
only the two ,i changed between the two calculation.


-- 
Xu Yuehua
physics Department of Nanjing university
China



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From njuxuyuehua at gmail.com  Sat Dec 15 15:10:35 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Sat, 15 Dec 2007 22:10:35 +0800
Subject: [Pw_forum] continue-help:E VS C curve gets worse when i enlarge
	encut and ..
Message-ID: <aca2feb20712150610x17b93024n90dec7cd5079e3bd@mail.gmail.com>

ECUT=35, ecutrho=210
C         E

2.77  -137.79732
2.78  -137.79749
2.8   -137.79773
2.81  -137.79778
2.82  -137.79783
2.83  -137.79783
2.84  -137.79781
2.85  -137.79774
2.86  -137.79769
encut=35,ecutrho=350
2.77 -137.79723
2.78  -137.79741
2.8   -137.79763
2.81  -137.79767
2.82  -137.79771
2.83  -137.79772
2.84  -137.79772
2.85  -137.79765
2.86  -137.7976
2.87  -137.79752
2.88  -137.7974

encut=40,ecutrho=400
2.77 -137.81067
2.78 -137.81076
2.8  -137.81102
2.81  -137.81101
2.82  -137.81096
2.83  -137.811
2.84  -137.81093
2.85  -137.81099
2.86  -137.81082
2.87  -137.81085


-- 
Xu Yuehua
physics Department of Nanjing university
China
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From kazempoor2000 at yahoo.com  Sat Dec 15 15:44:36 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sat, 15 Dec 2007 06:44:36 -0800 (PST)
Subject: [Pw_forum] pp.in
Message-ID: <248997.40874.qm@web33110.mail.mud.yahoo.com>

Dear All
 I want to plot charge density in the nanowire
supercell,but running pp.x takes much more time(1
day).Also I have 8 atoms in supercell and the size of
supercell is not big.why the calculation consume long
time? I attach pp.in:
&inputpp
    prefix  = 'MnAs1-1'
    outdir = '/scratch/home/akazem/tmp/MnAs/'
    filplot = 'MnAs1-1charge'
    plot_num= 0
    spin_component = 0 ,
 /
 &plot
    nfile = 1
    filepp(1) = 'MnAs1-1charge'
    weight(1) = 1.0
    iflag = 2
    output_format =2
    fileout = 'MnAs1-1.rho.dat'
    e1(1) =1.0, e1(2)=0.0, e1(3) = 0.0,
    e2(1) =0.0, e2(2)=1.0, e2(3) = 0.0,
    nx=15, ny=15
 /


thanks


      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping

From sohrab.ismail-beigi at yale.edu  Sat Dec 15 21:16:29 2007
From: sohrab.ismail-beigi at yale.edu (Sohrab Ismail-Beigi)
Date: Sat, 15 Dec 2007 15:16:29 -0500
Subject: [Pw_forum] Forces and finite electric fields (via Berry phase)
Message-ID: <03DAB48F-4372-4D55-B1C6-6A8D641A140C@yale.edu>

Dear users,

I've been experimenting with the addition of external electric fields  
via the Berry phase method with pw.x --- i.e. the type of electric  
field turned on by the input flag "lelfield" in conjunction with flags  
"lberry, gdir, nppstr, nberrcyc, efield".  After some hiccups  
(regarding k-point convergence and symmetry problems) and noticing  
that version 3.2.2 doesn't do this right (but the current CVS version  
apparently does), it seems that most of it works reasonably with one  
exception:

It seems that the atomic forces are missing the forces due to the  
external field --- a simple omission but one that causes the forces to  
be rather bizarre as written.  I've added a short fix to "forces.f90"  
inside the PW directory and I attach the modified forces.f90 file  
below.  But someone who knows more about the code should check that in  
fact this is not being done in duplicate (although after a careful  
perusing of the code, I don't see any other place the forces are added).

Has anyone else used this method successfully with pw.x and has some  
comments?  For example, it seems that the symmetries are handled a bit  
unusually when the field is turned on --- of course, with an external  
field, there are fewer symmetries but I'm not sure the ones it uses  
are the "right" ones (e.g. it generally reports only one symmetry  
[identity] in the output file but actually reduces the k-point set  
somewhat but not as much as when there is no field turned on).

Sincerely,

---------------------------------------------
Sohrab Ismail-Beigi
Associate Professor of Applied Physics and Physics
Dept. of Applied Physics
Yale University
P.O. Box 208284
New Haven, CT  06520
Phone: 203.432.2107
Fax: 203.432.4283
Email: sohrab.ismail-beigi at yale.edu
http://volga.eng.yale.edu/ - group home page
http://www.eng.yale.edu/aphy/ - dept. page w/ links
http://www.eng.yale.edu/graduate -- info about graduate studies in AP  
and brochures

P.S.  The forces.f90 file is attached below.  Note that this is based  
on what is in the CVS file --- corrections to espresso-3.2.2 are just  
the same with some minor changes to the "use" lines.  My corrections  
are identified by the "SIB".  There is also a debugging type "write"  
statement that should be removed for cleaner code...

!
! Copyright (C) 2001-2006 Quantum-ESPRESSO group
! This file is distributed under the terms of the
! GNU General Public License. See the file `License'
! in the root directory of the present distribution,
! or http://www.gnu.org/copyleft/gpl.txt .
!
#include "f_defs.h"
!
!----------------------------------------------------------------------------
SUBROUTINE forces()
   !----------------------------------------------------------------------------
   !
   ! ... This routine is a driver routine which computes the forces
   ! ... acting on the atoms. The complete expression of the forces
   ! ... contains four parts which are computed by different routines:
   !
   ! ...  a)  force_lc,    local contribution to the forces
   ! ...  b)  force_cc,    contribution due to NLCC
   ! ...  c)  force_ew,    contribution due to the electrostatic ewald  
term
   ! ...  d)  force_us,    contribution due to the non-local potential
   ! ...  e)  force_corr,  correction term for incomplete self- 
consistency
   ! ...  f)  force_hub,   contribution due to the Hubbard term
   !
   !
   USE kinds,         ONLY : DP
   USE io_global,     ONLY : stdout
   USE cell_base,     ONLY : at, bg, alat, omega
   USE ions_base,     ONLY : nat, nsp, ityp, tau, zv, amass
   USE gvect,         ONLY : ngm, gstart, nr1, nr2, nr3, nrx1, nrx2,  
nrx3, &
                             nrxx, ngl, nl, igtongl, g, gg, gcutm
   USE lsda_mod,      ONLY : nspin
   USE symme,         ONLY : s, nsym, irt
   USE vlocal,        ONLY : strf, vloc
   USE force_mod,     ONLY : force, lforce
   USE scf,           ONLY : rho
   USE ions_base,     ONLY : if_pos
   USE ldaU,          ONLY : lda_plus_u
   USE extfield,      ONLY : tefield, forcefield
   USE control_flags, ONLY : gamma_only, remove_rigid_rot, lbfgs

   ! SIB : added support for lelfield
   USE bp,               ONLY : lelfield, efield, gdir

   !
   IMPLICIT NONE
   !
   REAL(DP), ALLOCATABLE :: forcenl(:,:), &
                            forcelc(:,:), &
                            forcecc(:,:), &
                            forceion(:,:), &
                            forcescc(:,:), &
                            forceh(:,:)
     ! nonlocal, local, core-correction, ewald, scf correction terms,  
and hubbard
   REAL(DP) :: sumfor, sumscf, bnorm, bhat(3), flelfield
   INTEGER  :: ipol, na
     ! counter on polarization
     ! counter on atoms
   !
   !
   CALL start_clock( 'forces' )
   !
   ALLOCATE( forcenl( 3, nat ), forcelc( 3, nat ), forcecc( 3, nat ), &
             forceh( 3, nat ), forceion( 3, nat ), forcescc( 3, nat ) )
   !
   forcescc(:,:) = 0.D0
   forceh(:,:)   = 0.D0
   !
   WRITE( stdout, '(/,5x,"Forces acting on atoms (Ry/au):", / )')
   !
   ! ... The nonlocal contribution is computed here
   !
   CALL force_us( forcenl )
   !
   ! ... The local contribution
   !
   CALL force_lc( nat, tau, ityp, alat, omega, ngm, ngl, igtongl, &
                  nr1, nr2, nr3, nrx1, nrx2, nrx3, nrxx, g, rho%of_r,  
nl, &
                  nspin, gstart, gamma_only, vloc, forcelc )
   !
   ! ... The NLCC contribution
   !
   CALL force_cc( forcecc )
   !
   ! ... The Hubbard contribution
   !
   IF ( lda_plus_u ) CALL force_hub( forceh )
   !
   ! ... The ionic contribution is computed here
   !
   CALL force_ew( alat, nat, nsp, ityp, zv, at, bg, tau, omega, g, &
                  gg, ngm, gstart, gamma_only, gcutm, strf, forceion )
   !
   ! ... The SCF contribution
   !
   CALL force_corr( forcescc )
   !
   ! ... here we sum all the contributions and compute the total force  
acting
   ! ... on the crstal
   !
   DO ipol = 1, 3
      !
      sumfor = 0.D0
      !
      DO na = 1, nat
         !
         force(ipol,na) = forcenl(ipol,na)  + &
                          forceion(ipol,na) + &
                          forcelc(ipol,na)  + &
                          forcecc(ipol,na)  + &
                          forceh(ipol,na)   + &
                          forcescc(ipol,na)
         !
         IF ( tefield ) force(ipol,na) = force(ipol,na) +  
forcefield(ipol,na)
         !
         ! SIB : if lelfield is on, add force contribution on ions
         ! the 2.0 factor is because e^2=(electron charge)^2=2 in  
(Ryd,a0) units
         IF ( lelfield ) then
            bhat(:) = bg(:,gdir)
            bnorm = sqrt(dot_product(bhat(:),bhat(:)))
            bhat(:) = bhat(:)/bnorm
            flelfield = 2.0d0*zv(ityp(na))*efield*bhat(ipol)
            write( stdout , '(a,x,i1,3x,a,i5,3x,3(a,f13.9,3x))' ) &
                   'axis',ipol,'atom',na,'fprelel',force(ipol,na), &
                   'flel',flelfield,'ftot',force(ipol,na)+flelfield
            force(ipol,na) = force(ipol,na) + flelfield
         END IF
         !
         sumfor = sumfor + force(ipol,na)
         !
      END DO
      !
      ! ... impose total force = 0
      !
      DO na = 1, nat
         !
         force(ipol,na) = force(ipol,na) - sumfor / DBLE( nat )
         !
      END DO
      !
   END DO
   !
   ! ... resymmetrize (should not be needed, but ...)
   !
   IF ( nsym >= 1 ) THEN
      !
      DO na = 1, nat
         CALL trnvect( force(1,na), at, bg, - 1 )
      END DO
      !
      CALL symvect( nat, force, nsym, s, irt )
      !
      DO na = 1, nat
         CALL trnvect( force(1,na), at, bg, 1 )
      END DO
      !
   END IF
   !
   IF ( remove_rigid_rot ) &
      CALL remove_tot_torque( nat, tau, amass(ityp(:)), force  )
   !
   ! ... write on output the forces
   !
   DO na = 1, nat
      !
      WRITE( stdout, 9035) na, ityp(na), force(:,na)
      !
   END DO
   !
   ! ... forces on fixed coordinates are set to zero ( C.S. 15/10/2003 )
   !
   force(:,:)    = force(:,:)    * DBLE( if_pos )
   forcescc(:,:) = forcescc(:,:) * DBLE( if_pos )
   !
#if defined (DEBUG)
   !
   WRITE( stdout, '(5x,"The non-local contrib.  to forces")')
   DO na = 1, nat
      WRITE( stdout, 9035) na, ityp(na), ( forcenl(ipol,na), ipol = 1,  
3 )
   END DO
   WRITE( stdout, '(5x,"The ionic contribution  to forces")')
   DO na = 1, nat
      WRITE( stdout, 9035) na, ityp(na), ( forceion(ipol,na), ipol =  
1, 3 )
   END DO
   WRITE( stdout, '(5x,"The local contribution  to forces")')
   DO na = 1, nat
      WRITE( stdout, 9035) na, ityp(na), ( forcelc(ipol,na), ipol = 1,  
3 )
   END DO
   WRITE( stdout, '(5x,"The Hubbard contrib.    to forces")')
   DO na = 1, nat
      WRITE( stdout, 9035) na, ityp(na), ( forceh(ipol,na), ipol = 1,  
3 )
   END DO
   WRITE( stdout, '(5x,"The SCF correction term to forces")')
   DO na = 1, nat
      WRITE( stdout, 9035) na, ityp(na), ( forcescc(ipol,na), ipol =  
1, 3 )
   END DO
   !
#endif
   !
   sumfor = 0.D0
   sumscf = 0.D0
   !
   DO na = 1, nat
      !
      sumfor = sumfor + &
               force(1,na)**2 + force(2,na)**2 + force(3,na)**2
      !
      sumscf = sumscf + &
               forcescc(1,na)**2 + forcescc(2,na)**2+ forcescc(3,na)**2
      !
   END DO
   !
   sumfor = SQRT( sumfor )
   sumscf = SQRT( sumscf )

   WRITE( stdout, '(/5x,"Total force = ",F12.6,5X, &
               &  "Total SCF correction = ",F12.6)') sumfor, sumscf
   !
   DEALLOCATE( forcenl, forcelc, forcecc, forceh, forceion, forcescc )
   !
   lforce = .TRUE.
   !
   CALL stop_clock( 'forces' )
   !
   IF ( lbfgs .AND. ( sumfor < 10.D0*sumscf ) ) &
   WRITE( stdout,'(5x,"SCF correction compared to forces is too large,  
reduce conv_thr")')
!     CALL errore( 'forces', 'scf correction on ' // &
!                & 'the force is too large: reduce conv_thr', 1 )
   !
   RETURN
   !
9035 FORMAT(5X,'atom ',I3,' type ',I2,'   force = ',3F14.8)
   !
END SUBROUTINE forces



From w2agz at pacbell.net  Sun Dec 16 05:50:01 2007
From: w2agz at pacbell.net (Paul M. Grant)
Date: Sat, 15 Dec 2007 20:50:01 -0800
Subject: [Pw_forum] Optical properties
In-Reply-To: <397690649.25502@mail.sdu.edu.cn>
References: <397513651.07592@mail.sdu.edu.cn> <397533402.31255@mail.sdu.edu.cn>
	<397690649.25502@mail.sdu.edu.cn>
Message-ID: <003401c83f9f$1e9106b0$5bb31410$@net>

Dear Kesong,

 

I have successfully tested Andrea's epsilon.x against aluminum under
QE-3.2.3.  There is a problem with the off-diagonal elements (which should
be zero for a cubic symmetry) and I don't know if he's had a chance to fix
that yet.  For cubic systems, the code works fine.

 

-Paul Grant

 

Paul M. Grant, PhD

Principal, W2AGZ Technologies

Visiting Scholar, Applied Physics, Stanford University

EPRI Science Fellow (Retired)

IBM Research Staff Member Emeritus

 <mailto:w2agz at pacbell.net> w2agz at pacbell.net

 <http://www.w2agz.com/> http://www.w2agz.com

 

 

 

From: pw_forum-bounces at pwscf.org [mailto:pw_forum-bounces at pwscf.org] On
Behalf Of yupiaofei(SDU)
Sent: Friday, December 14, 2007 7:45 PM
To: PWSCF Forum
Subject: Re: [Pw_forum] Optical properties

 

Dear Andrea,

 

According to your guidance, I compiled the epsilon.x successfully, but I
have two questions,

 

i.  I tested the epsilon.x, and it could read the outputfile by PWSCF3.2.
However, it can't read the save file by 

PW3.0. Is that true?

 

ii. The epsilon.x cann't support the ultra soft PP?

 

 

sincerely

 

Kesong Yang

 

School of Physics and Microelectronics

 

Shandong University, Jinan 250100, People's Republic of China

 

 

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From oulihui666 at 126.com  Sun Dec 16 10:06:48 2007
From: oulihui666 at 126.com (oulihui666)
Date: Sun, 16 Dec 2007 17:06:48 +0800 (CST)
Subject: [Pw_forum] A problem about pdos
Message-ID: <12175848.756821197796008207.JavaMail.coremail@bj126app104.126.com>

Dear pwscf users,
   I have a question, quite naive. I tried to search the pdos of oxygen molecular, 
but I have to rely on your advice. as well as I know,the calculation procedes as 
follows:
1) make a self-consistent calculation (input=O2.scf.in)
2) run a non-self-consistent calculation (input=O2.nscf.in)
3) run projwfc.x program (input=O2.pdos.in, output=O2.pdos.out)in order to produce a 
postscript file: O2.pdos_tot.
    After scf and nscf calculation, the program pdos was used as follows:
&CONTROL
 1)scf calculation:              
                 calculation = 'scf' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/olh/tmp/' ,
                  pseudo_dir = '/home/olh/pseudo/' ,
                      prefix = 'O2' ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 10.486,
                   celldm(3) = 2.979,
                         nat = 2,
                        ntyp = 1,
                     ecutwfc = 30 ,
                     ecutrho = 300 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.5,
 /
 &ELECTRONS
                    conv_thr = 1.D-6 ,
                 mixing_beta = 0.4D0 ,
             diagonalization = 'david' ,
 /
ATOMIC_SPECIES
    O   15.99900  O.pbe-rrkjus.UPF 
ATOMIC_POSITIONS angstrom 
    O     -1.553621017    5.696221321    6.037977498    0  0  0 
    O     -2.611378983    6.337778679    6.038022502    0  0  0 
K_POINTS automatic 
  4 4 1   1 1 1 
2) nscf calculation:
 &CONTROL
                 calculation = 'nscf' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/olh/tmp/' ,
                  pseudo_dir = '/home/olh/pseudo/' ,
                      prefix = 'O2' ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 10.486,
                   celldm(3) = 2.979,
                         nat = 2,
                        ntyp = 1,
                     ecutwfc = 30 ,
                     ecutrho = 300 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.5,
 /
 &ELECTRONS
                    conv_thr = 1.D-6 ,
                 mixing_beta = 0.4D0 ,
             diagonalization = 'david' ,
 /
ATOMIC_SPECIES
    O   15.99900  O.pbe-rrkjus.UPF 
ATOMIC_POSITIONS angstrom 
    O     -1.553621017    5.696221321    6.037977498    0  0  0 
    O     -2.611378983    6.337778679    6.038022502    0  0  0 
K_POINTS automatic 
  4 4 1   1 1 1
3) pdos calculation: 
 &INPUTPP
                      prefix = 'O2' ,
                      outdir = '/home/olh/tmp/' ,
                      ngauss = 1,
                     degauss = 0.02,
                      DeltaE = 0.01 ,
                        Emin = -35 ,
                        Emax = -4 ,
 /
    However, when I calculated pdos, in order to produce a postscript file: 
O2.pdos_tot, I encounter a problem, output is displayed as follows:
.....
k =  -0.3750000000 -0.2165063509  0.1678415576
     e =   -30.88771 eV
     psi = 
    |psi|^2 =   NaN
     e =   -18.42806 eV
     psi = 
    |psi|^2 =   NaN
     e =   -12.12292 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.97042 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.96565 eV
     psi = 
    |psi|^2 =   NaN
     e =    -4.27073 eV
     psi = 
    |psi|^2 =   NaN
 k =   0.0000000000 -0.4330127019 -0.1678415576
     e =   -30.88770 eV
     psi = 
    |psi|^2 =   NaN
     e =   -18.42864 eV
     psi = 
    |psi|^2 =   NaN
     e =   -12.12059 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.96946 eV
     psi = 
    |psi|^2 =   NaN
     e =   -10.96552 eV
     psi = 
    |psi|^2 =   NaN
     e =    -4.27538 eV
     psi = 
    |psi|^2 =   NaN
Lowdin Charges: 
     Atom #   1: total charge =      NaN, s, p, d, f =      NaN     NaN
                 spin up      =      NaN, s, p, d, f =      NaN     NaN
                 spin down    =      NaN, s, p, d, f =      NaN     NaN
                 polarization =      NaN, s, p, d, f =      NaN     NaN
     Atom #   2: total charge =      NaN, s, p, d, f =      NaN     NaN
                 spin up      =      NaN, s, p, d, f =      NaN     NaN
                 spin down    =      NaN, s, p, d, f =      NaN     NaN
                 polarization =      NaN, s, p, d, f =      NaN     NaN
     Spilling Parameter:      NaN
It displayed "NaN", not numerical, I am confused.
Any suggestions is appreciated.
 
Thank you in advance
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 umari at democritos.it  Sun Dec 16 12:20:47 2007
From: umari at democritos.it (umari at democritos.it)
Date: Sun, 16 Dec 2007 12:20:47 +0100
Subject: [Pw_forum] Forces and finite electric fields (via Berry phase)
Message-ID: <20071216122047.kwy8l3vz8gg0ccwc@mail.democritos.it>

Dear Ismail,

You are right the ionic term on the atomic forces was missing.

At the moment the Berry's phase electric field is supposed to work
without using the symmetry of the k-points (option: nosym=.true. ).
With the CVS version the options gdir=1 and gdir=2 should work
also on parallel machines.
Note that in the case of US pseudopotentials the  extra term which arises for
the electronic contribution to the atomic forces is not implemented yet
(although I plan to code this in the next 1-2 weeks).
However, the term is correctly treated in the cp.x code.


Best wishes,

Paolo Umari

Democritos

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From ferretti.andrea at unimore.it  Sun Dec 16 20:03:19 2007
From: ferretti.andrea at unimore.it (Andrea Ferretti)
Date: Sun, 16 Dec 2007 20:03:19 +0100 (CET)
Subject: [Pw_forum] Optical properties
In-Reply-To: <397690649.25502@mail.sdu.edu.cn>,
	<002101c83ecc$dcba3360$5120c2ca@flysky>
References: <397513651.07592@mail.sdu.edu.cn> <397533402.31255@mail.sdu.edu.cn>
	<397690649.25502@mail.sdu.edu.cn>,
	<002101c83ecc$dcba3360$5120c2ca@flysky>
Message-ID: <Pine.LNX.4.64.0712161950390.21400@lichene.fisica.unimo.it>



Dear Kesong,


> i.  I tested the epsilon.x, and it could read the outputfile by PWSCF3.2. 
> However, it can't read the save file by PW3.0. Is that true?

this is correct, 
the format of the restart file used to change rapidly from one version to 
another... since espresso-3.2 it is instead indented to be much more 
stable and it should be readable also by the next coming versions

> 
> ii. The epsilon.x cann't support the ultra soft PP?
> 

at the moment USPP are not supported: epsilon.x computes the matrix 
elements of the momentum p which are difficult to "augment" in the USPP 
framework (at least within the data stored in the current 
UPF pseudopotential format)...
for the future, note that QE is going to support PAW which is eg one way to 
shortcut the problem

note also that the corrections due to the nonlocal terms in the 
pseudopotentials are not accounted for;

all the best
andrea  


Andrea Ferretti
National Research Center S3, CNR-INFM  ( http://s3.infm.it )
Dip. Fisica, Univ. di Modena e Reggio E. (Italy)
Tel: +39 059 2055301;  Fax: +39 059 374794;  Skype: andrea_ferretti
URL: http://www.nanoscience.unimo.it

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

From kazempoor2000 at yahoo.com  Mon Dec 17 07:46:04 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sun, 16 Dec 2007 22:46:04 -0800 (PST)
Subject: [Pw_forum] hamiltonian matrix
Message-ID: <884235.88039.qm@web33115.mail.mud.yahoo.com>

Dear all
Where(which output) can i find the hamiltonian matrix
?
for solving kohn -sham equation,by which method are
used to obtain V (electron-ion)?
thanks 



      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From ceresoli at sissa.it  Mon Dec 17 12:16:47 2007
From: ceresoli at sissa.it (Davide Ceresoli)
Date: Mon, 17 Dec 2007 12:16:47 +0100
Subject: [Pw_forum] Could PWscf code handle the atom or molecule in
 external magnetic field ?
In-Reply-To: <480522.74293.qm@web73008.mail.tp2.yahoo.com>
References: <480522.74293.qm@web73008.mail.tp2.yahoo.com>
Message-ID: <47665A9F.2080302@sissa.it>

? ?? wrote:
> Dear forum's members,
> 
> I wonder could PWscf code handle the atom or molecule
> in external magnetic field ?
The quick answer is:
finite magnetic field -> NO (not yet!)
vanishing magnetic field -> YES (in perturbation theory, via the GIPAW code).

Davide

-- 
+----------------------------------------------------------+
   Davide Ceresoli <ceresoli at sissa.it>
   Scuola Internazionale Superiore di Studi Avanzati (SISSA)
   via Beirut 2-4
   I-34014 Trieste, Italy
   Phone: +39-040-3787-448  Fax: +39-040-3787-528
   Mobile: +39-347-1001570
   Skype: dceresoli
   Homepage: http://people.sissa.it/~ceresoli
+----------------------------------------------------------+

From degironc at sissa.it  Mon Dec 17 12:33:57 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Mon, 17 Dec 2007 12:33:57 +0100
Subject: [Pw_forum] hamiltonian matrix
In-Reply-To: <884235.88039.qm@web33115.mail.mud.yahoo.com>
References: <884235.88039.qm@web33115.mail.mud.yahoo.com>
Message-ID: <47665EA5.5030805@sissa.it>

ali kazempoor wrote:
> Dear all
> Where(which output) can i find the hamiltonian matrix
> ?
>   
nowhere
> for solving kohn -sham equation,by which method are
> used to obtain V (electron-ion)?
> thanks 
>
>   
h_psi.f90,  v_of_rho.f90

stefano
>
>       ____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page. 
> http://www.yahoo.com/r/hs
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From benassi.a at gmail.com  Mon Dec 17 12:39:30 2007
From: benassi.a at gmail.com (Andrea Benassi)
Date: Mon, 17 Dec 2007 12:39:30 +0100
Subject: [Pw_forum] Optical properties
In-Reply-To: <Pine.LNX.4.64.0712161950390.21400@lichene.fisica.unimo.it>
References: <397513651.07592@mail.sdu.edu.cn> <397533402.31255@mail.sdu.edu.cn>
	<397690649.25502@mail.sdu.edu.cn>
	<002101c83ecc$dcba3360$5120c2ca@flysky>
	<Pine.LNX.4.64.0712161950390.21400@lichene.fisica.unimo.it>
Message-ID: <97c430b70712170339q7fc536edg1d50d560e02b03dc@mail.gmail.com>

I'll fix the bug on the off-diagonal components of the dielectric tensor
during Christmas holidays, check the new CVS version on January!
Best wishes.
Andrea

-- 
Andrea Benassi
National Research Center S3, CNR-INFM  ( http://www.s3.infm.it )
Dipartimento di Fisica, Universita' di Modena e Reggio Emilia
Via Campi 213/A I-41100 Modena, Italy
Tel:     +39 059 2055314
Fax:     +39 059 374794
E-mail:  benassi.andrea at unimore.it
URL:     http://www.nanoscience.unimo.it
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From chen_shao_hua197 at yahoo.com.tw  Mon Dec 17 13:34:31 2007
From: chen_shao_hua197 at yahoo.com.tw (=?big5?q?=B3=AF=20=A4=D6=B5=D8?=)
Date: Mon, 17 Dec 2007 20:34:31 +0800 (CST)
Subject: [Pw_forum] Could PWscf code handle the atom or molecule in
	external magnetic field ?
In-Reply-To: <47665A9F.2080302@sissa.it>
Message-ID: <798141.46457.qm@web73011.mail.tp2.yahoo.com>

I see.
Thanks for your reply.

max
Physics department, National Taiwan University, Taiwan


--- Davide Ceresoli <ceresoli at sissa.it> ??

> ? ?? wrote:
> > Dear forum's members,
> > 
> > I wonder could PWscf code handle the atom or
> molecule
> > in external magnetic field ?
> The quick answer is:
> finite magnetic field -> NO (not yet!)
> vanishing magnetic field -> YES (in perturbation
> theory, via the GIPAW code).
> 
> Davide
> 
> -- 
>
+----------------------------------------------------------+
>    Davide Ceresoli <ceresoli at sissa.it>
>    Scuola Internazionale Superiore di Studi Avanzati
> (SISSA)
>    via Beirut 2-4
>    I-34014 Trieste, Italy
>    Phone: +39-040-3787-448  Fax: +39-040-3787-528
>    Mobile: +39-347-1001570
>    Skype: dceresoli
>    Homepage: http://people.sissa.it/~ceresoli
>
+----------------------------------------------------------+
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 



      ______________________________________________________________________________________
??????????????????????????????http://tw.promo.yahoo.com/antispam/index.html

From giannozz at nest.sns.it  Mon Dec 17 14:17:12 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 17 Dec 2007 14:17:12 +0100
Subject: [Pw_forum] pp.in
In-Reply-To: <248997.40874.qm@web33110.mail.mud.yahoo.com>
References: <248997.40874.qm@web33110.mail.mud.yahoo.com>
Message-ID: <B064C337-52AE-4020-BC67-29E1202A7F53@nest.sns.it>


On Dec 15, 2007, at 15:44 , ali kazempoor wrote:

> I want to plot charge density in the nanowire supercell,
> but running pp.x takes much more time(1 day). Also I
> have 8 atoms in supercell and the size of supercell is
> not big. Why the calculation consume long time?

plots can be really slow if the charge density is recalculated in
real space for all points (see description of iflag=3 case in the
INPUT_PP file). The data you sent is for a 15x15 2-d plot and
I am not going to believe that it requires one day unless I see it

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 nest.sns.it  Mon Dec 17 15:12:15 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 17 Dec 2007 15:12:15 +0100
Subject: [Pw_forum] A problem about pdos
In-Reply-To: <12175848.756821197796008207.JavaMail.coremail@bj126app104.126.com>
References: <12175848.756821197796008207.JavaMail.coremail@bj126app104.126.com>
Message-ID: <131A7713-5777-47EC-9327-6EBEDE8F8F29@nest.sns.it>


On Dec 16, 2007, at 10:06 , oulihui666 wrote:

> However, when I calculated pdos, in order to produce a postscript  
> file:
> O2.pdos_tot, I encounter a problem, output is displayed as follows:
> ......
> k =  -0.3750000000 -0.2165063509  0.1678415576
>      e =   -30.88771 eV
>      psi =
>     |psi|^2 =   NaN

it works for me (both the 3.2.3 and the CVS versions)

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 nest.sns.it  Mon Dec 17 15:38:54 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Mon, 17 Dec 2007 15:38:54 +0100
Subject: [Pw_forum] Raman and IR intensities for a metal
In-Reply-To: <043BD905-AA7A-42B3-8E7F-FA9497DF3E4C@sissa.it>
References: <20071214191837.ezu180ga8sgkcs40@www.staffmail.ed.ac.uk>
	<043BD905-AA7A-42B3-8E7F-FA9497DF3E4C@sissa.it>
Message-ID: <1AC7BF2E-7811-455A-B848-E67A9D43E1A9@nest.sns.it>


On Dec 14, 2007, at 22:46 , Stefano Baroni wrote:

> According to the usual theory, they both should be zero:
> the second is given by Born effective charges (that are
> zero in metals), the former by the derivative of the inverse
> macroscopic electric constant (which is also zero). How
> can a metal be Raman or IR active?

a true metal cannot, but there cases of systems that are
considered as "metallic" and still exhibit both Raman and
IR active modes: K_3C_60, for instance

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 mmarques at staffmail.ed.ac.uk  Mon Dec 17 17:05:41 2007
From: mmarques at staffmail.ed.ac.uk (Miriam Marques)
Date: Mon, 17 Dec 2007 16:05:41 +0000
Subject: [Pw_forum] Raman and IR intensities
Message-ID: <20071217160541.mqujm0jx8gggwokg@www.staffmail.ed.ac.uk>


On Dec 17, 2007, at 15:38 , Paolo Giannozzi wrote

> a true metal cannot, but there cases of systems that are
> considered as "metallic" and still exhibit both Raman and
> IR active modes: K_3C_60, for instance


  There are also some references about Raman active modes for hcp metals
  (Fe, Zn, Zr, Mg) (Science 288, 1626 (2000))
  and a high-pressure metallic phase of oxygen (Phys. Rev. B 76, 64101 (2007).

  I was wondering how to obtain the Raman intensities for
  such "metallic"  materials.
  Any suggestion?

  Thank you very much,

  Miriam.


  Dr. Miriam Marques
  Centre for Science at Extreme Conditions.
  The University of Edinburgh.
  e-mail: mmarques at staffmail.ed.ac.uk


-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.



From sunshoutian168 at yahoo.com.cn  Tue Dec 18 02:00:41 2007
From: sunshoutian168 at yahoo.com.cn (shoutian sun)
Date: Tue, 18 Dec 2007 09:00:41 +0800 (CST)
Subject: [Pw_forum] The perseudoes
Message-ID: <840345.84412.qm@web92010.mail.cnb.yahoo.com>

>Dear all,
>there are a lot of  perseudo potential, which one is the best?




      ___________________________________________________________ 
?????????????????? 
http://cn.mail.yahoo.com/promo/taobao20/index.php
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From marzari at MIT.EDU  Tue Dec 18 09:11:27 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Tue, 18 Dec 2007 03:11:27 -0500
Subject: [Pw_forum] The perseudoes
In-Reply-To: <840345.84412.qm@web92010.mail.cnb.yahoo.com>
References: <840345.84412.qm@web92010.mail.cnb.yahoo.com>
Message-ID: <476780AF.3060905@mit.edu>

shoutian sun wrote:
>  >Dear all,
>  >there are a lot of  perseudo potential, which one is the best?


I like them all.

			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 akohlmey at cmm.chem.upenn.edu  Wed Dec 19 01:03:37 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 18 Dec 2007 19:03:37 -0500 (EST)
Subject: [Pw_forum] The perseudoes
In-Reply-To: <840345.84412.qm@web92010.mail.cnb.yahoo.com>
References: <840345.84412.qm@web92010.mail.cnb.yahoo.com>
Message-ID: <Pine.LNX.4.64.0712181859440.2798@localhost.localdomain>

On Tue, 18 Dec 2007, shoutian sun wrote:

SS> >Dear all,
>there are a lot of  perseudo potential, which one is the best?


the one that gives you the correct answer!!

unfortunately, that depends a lot on what you
want to do, so you may have to try and test 
them all...

... if you do. please let us known which ones
worked best for you and what you used them for.

thanks,
  axel.





      ___________________________________________________________ 
???????????????????????????????????? 
http://cn.mail.yahoo.com/promo/taobao20/index.php

-- 
=======================================================================
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 wangzhentang at gmail.com  Wed Dec 19 04:32:13 2007
From: wangzhentang at gmail.com (zhentang wang)
Date: Wed, 19 Dec 2007 11:32:13 +0800
Subject: [Pw_forum] relax question
Message-ID: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com>

Dear pwscf users,

I  am runing in  parallel a relax conculation ,and there are some problems
to ask.

cluster  Set up

pwscf  versin:      3.2.3

 compiler:             ifort     I_fc_p_10.0.23     mkl9.1.023

mpi:                       moich2-1.0.06
system :                cluster xeon 5345 (64bit)

Input
&control
    calculation='relax',
    restart_mode='from_scratch',
    prefix='GaMnAs',
    pseudo_dir = '/home/ztwang/PP',
    outdir='tmp',
    tprnfor=.true.,
    disk_io='high',
    verbosity='high',
/
 &system
    ibrav=1, celldm(1) = 21.0,
    nat=65, ntyp=3,
    ecutwfc=60,
    ecutrho=360.0,
    starting_magnetization(1)=0.3,
    starting_magnetization(2)=0.0,
    nspin=2,
    occupations='smearing',
    degauss=0.02,
    smearing='cold',
/
&electrons
     mixing_beta = 0.5
     conv_thr =  1.0d-6
     mixing_mode='local-TF'
/
&ions
//
ATOMIC_SPECIES
  Mn   54.938049  MnPZus_15e.vdb.DB.UPF
 Ga    69.723    Ga.pz-bhs.UPF
 As   74.92160   As.pz-bhs.UPF
ATOMIC_POSITIONS
Mn      0.250000000     0.250000000      0.250000000
Ga      0.000000000     0.000000000      0.000000000
Ga      0.000000000      0.250000000      0.250000000
Ga      0.250000000     0.000000000      0.250000000
Ga      0.250000000     0.250000000      0.000000000
As      0.125000000     0.125000000      0.125000000
As      0.125000000      0.375000000      0.375000000
As      0.375000000     0.125000000      0.375000000
As      0.375000000     0.375000000      0.125000000
Ga      0.000000000     0.000000000      0.500000000
Ga      0.000000000      0.250000000      0.750000000
Ga      0.250000000     0.000000000      0.750000000
Ga      0.250000000     0.250000000      0.500000000
As      0.125000000     0.125000000      0.625000000
As      0.125000000      0.375000000      0.875000000
As      0.375000000     0.125000000      0.875000000
As      0.375000000     0.375000000      0.625000000
Ga      0.000000000     0.500000000      0.000000000
Ga      0.000000000      0.750000000      0.250000000
Ga      0.250000000     0.500000000      0.250000000
Ga      0.250000000     0.750000000      0.000000000
As      0.125000000     0.625000000      0.125000000
As      0.125000000      0.875000000      0.375000000
As      0.375000000     0.625000000      0.375000000
As      0.375000000     0.875000000      0.125000000
Ga      0.000000000     0.500000000      0.500000000
Ga      0.000000000      0.750000000      0.750000000
Ga      0.250000000     0.500000000      0.750000000
Ga      0.250000000     0.750000000      0.500000000
As      0.125000000     0.625000000      0.625000000
As      0.125000000      0.875000000      0.875000000
As      0.375000000     0.625000000      0.875000000
As      0.375000000     0.875000000      0.625000000
Ga      0.500000000     0.000000000      0.000000000
Ga      0.500000000      0.250000000      0.250000000
Ga      0.750000000     0.000000000      0.250000000
Ga      0.750000000     0.250000000      0.000000000
As      0.625000000     0.125000000      0.125000000
As      0.625000000      0.375000000      0.375000000
As      0.875000000     0.125000000      0.375000000
As      0.875000000     0.375000000      0.125000000
Ga      0.500000000     0.000000000      0.500000000
Ga      0.500000000      0.250000000      0.750000000
Ga      0.750000000     0.000000000      0.750000000
Ga      0.750000000     0.250000000      0.500000000
As      0.625000000     0.125000000      0.625000000
As      0.625000000      0.375000000      0.875000000
As      0.875000000     0.125000000      0.875000000
As      0.875000000     0.375000000      0.625000000
Ga      0.500000000     0.500000000      0.000000000
Ga      0.500000000      0.750000000      0.250000000
Ga      0.750000000     0.500000000      0.250000000
Ga      0.750000000     0.750000000      0.000000000
As      0.625000000     0.625000000      0.125000000
As      0.625000000      0.875000000      0.375000000
As      0.875000000     0.625000000      0.375000000
As      0.875000000     0.875000000      0.125000000
Ga      0.500000000     0.500000000      0.500000000
Ga      0.500000000      0.750000000      0.750000000
Ga      0.750000000     0.500000000      0.750000000
Ga      0.750000000     0.750000000      0.500000000
As      0.625000000     0.625000000      0.625000000
As      0.625000000      0.875000000      0.875000000
As      0.875000000     0.625000000      0.875000000
As      0.875000000     0.875000000      0.625000000
K_POINTS {automatic}
2 2 2 1 1 1

error information was found, it displyed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
End of self-consistent calculation
convergence NOT achieved, stopping
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>

And then I  change ecutwfc=40,ecutrho=200.0
error information was found, it displyed
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #       679
     info =/= 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
rank 0 in job 16  node01_33013   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
And then I  change ecutwfc=22,ecutrho=100.0,there is also no problem.but I
think total energy may be not  accurate.
I  wonder if this is a problem with the system or a problem of the
grogram(MPI) or a problem with input setting.




Thank you very much in advance,

Best  regards
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From degironc at sissa.it  Wed Dec 19 10:12:47 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Wed, 19 Dec 2007 10:12:47 +0100
Subject: [Pw_forum] relax question
In-Reply-To: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com>
References: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com>
Message-ID: <4768E08F.20204@sissa.it>

the first error is related to a scf calculation that did not 
converged...this may be due to various causes. have you checked that the 
atomic configuration is reasonable and non atoms overlap ?
the second error is an error in diagonalization ... it means that your 
hamiltonian is probably corrupted or very strange ... have you checked 
that the atomic configuration is reasonable and non atoms overlap ?
22 + 100 Ry should be reasonable for Ga and As but  are probably  too 
small for Mn

stefano


zhentang wang wrote:
> Dear pwscf users,
>
> I  am runing in  parallel a relax conculation ,and there are some 
> problems to ask.
>  
> cluster  Set up
>
> pwscf  versin:      3.2.3
>
>  compiler:             ifort     I_fc_p_10.0.23     mkl9.1.023
>
> mpi:                       moich2-1.0.06
> system :                cluster xeon 5345 (64bit)
>
> Input
> &control
>     calculation='relax',
>     restart_mode='from_scratch',
>     prefix='GaMnAs',
>     pseudo_dir = '/home/ztwang/PP',
>     outdir='tmp',
>     tprnfor=.true.,
>     disk_io='high',
>     verbosity='high',
> /
>  &system
>     ibrav=1, celldm(1) = 21.0,
>     nat=65, ntyp=3,
>     ecutwfc=60,
>     ecutrho=360.0,
>     starting_magnetization(1)=0.3,
>     starting_magnetization(2)=0.0,
>     nspin=2,
>     occupations='smearing',
>     degauss=0.02,
>     smearing='cold',
> /
> &electrons
>      mixing_beta = 0.5
>      conv_thr =  1.0d-6
>      mixing_mode='local-TF'
> /
> &ions
> //
> ATOMIC_SPECIES
>   Mn   54.938049  MnPZus_15e.vdb.DB.UPF
>  Ga    69.723    Ga.pz-bhs.UPF
>  As   74.92160   As.pz-bhs.UPF
> ATOMIC_POSITIONS
> Mn      0.250000000     0.250000000      0.250000000
> Ga      0.000000000     0.000000000      0.000000000
> Ga      0.000000000      0.250000000      0.250000000
> Ga      0.250000000     0.000000000      0.250000000
> Ga      0.250000000     0.250000000      0.000000000
> As      0.125000000     0.125000000      0.125000000
> As      0.125000000      0.375000000      0.375000000
> As      0.375000000     0.125000000      0.375000000
> As      0.375000000     0.375000000      0.125000000
> Ga      0.000000000     0.000000000      0.500000000
> Ga      0.000000000      0.250000000      0.750000000
> Ga      0.250000000     0.000000000      0.750000000
> Ga      0.250000000     0.250000000      0.500000000
> As      0.125000000     0.125000000      0.625000000
> As      0.125000000      0.375000000      0.875000000
> As      0.375000000     0.125000000      0.875000000
> As      0.375000000     0.375000000      0.625000000
> Ga      0.000000000     0.500000000      0.000000000
> Ga      0.000000000      0.750000000      0.250000000
> Ga      0.250000000     0.500000000      0.250000000
> Ga      0.250000000     0.750000000      0.000000000
> As      0.125000000     0.625000000      0.125000000
> As      0.125000000      0.875000000      0.375000000
> As      0.375000000     0.625000000      0.375000000
> As      0.375000000     0.875000000      0.125000000
> Ga      0.000000000     0.500000000      0.500000000
> Ga      0.000000000      0.750000000      0.750000000
> Ga      0.250000000     0.500000000      0.750000000
> Ga      0.250000000     0.750000000      0.500000000
> As      0.125000000     0.625000000      0.625000000
> As      0.125000000      0.875000000      0.875000000
> As      0.375000000     0.625000000      0.875000000
> As      0.375000000     0.875000000      0.625000000
> Ga      0.500000000     0.000000000      0.000000000
> Ga      0.500000000      0.250000000      0.250000000
> Ga      0.750000000     0.000000000      0.250000000
> Ga      0.750000000     0.250000000      0.000000000
> As      0.625000000     0.125000000      0.125000000
> As      0.625000000      0.375000000      0.375000000
> As      0.875000000     0.125000000      0.375000000
> As      0.875000000     0.375000000      0.125000000
> Ga      0.500000000     0.000000000      0.500000000
> Ga      0.500000000      0.250000000      0.750000000
> Ga      0.750000000     0.000000000      0.750000000
> Ga      0.750000000     0.250000000      0.500000000
> As      0.625000000     0.125000000      0.625000000
> As      0.625000000      0.375000000      0.875000000
> As      0.875000000     0.125000000      0.875000000
> As      0.875000000     0.375000000      0.625000000
> Ga      0.500000000     0.500000000      0.000000000
> Ga      0.500000000      0.750000000      0.250000000
> Ga      0.750000000     0.500000000      0.250000000
> Ga      0.750000000     0.750000000      0.000000000
> As      0.625000000     0.625000000      0.125000000
> As      0.625000000      0.875000000      0.375000000
> As      0.875000000     0.625000000      0.375000000
> As      0.875000000     0.875000000      0.125000000
> Ga      0.500000000     0.500000000      0.500000000
> Ga      0.500000000      0.750000000      0.750000000
> Ga      0.750000000     0.500000000      0.750000000
> Ga      0.750000000     0.750000000      0.500000000
> As      0.625000000     0.625000000      0.625000000
> As      0.625000000      0.875000000      0.875000000
> As      0.875000000     0.625000000      0.875000000
> As      0.875000000     0.875000000      0.625000000
> K_POINTS {automatic}
> 2 2 2 1 1 1
>
> error information was found, it displyed
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> End of self-consistent calculation
> convergence NOT achieved, stopping
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
>
> And then I  change ecutwfc=40,ecutrho=200.0
> error information was found, it displyed
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> %%%%%%%%%%%%%%%%%%%%%%%%%%
>      from cdiaghg : error #       679
>      info =/= 0
> %%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
> rank 0 in job 16  node01_33013   caused collective abort of all ranks
>   exit status of rank 0: killed by signal 9
> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> And then I  change ecutwfc=22,ecutrho=100.0,there is also no 
> problem.but I think total energy may be not  accurate.
> I  wonder if this is a problem with the system or a problem of the 
> grogram(MPI) or a problem with input setting.
>
>
>
>
> Thank you very much in advance,
>
> Best  regards
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From oulihui666 at 126.com  Wed Dec 19 13:30:03 2007
From: oulihui666 at 126.com (oulihui666)
Date: Wed, 19 Dec 2007 20:30:03 +0800 (CST)
Subject: [Pw_forum] About NEB restart
Message-ID: <23594730.634771198067403681.JavaMail.coremail@bj126app103.126.com>

Dear pwscf users,
    Recently, I encounter a problem about neb, I intend to calculate the neb about adsorption, unfortunately, power cut, so I want to restart the calculation following interrupted task by using 'restart', but when I restart the calculation, error information is displayed. 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #       238
     info =/= 0
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
p0_3953:  p4_error: : 0
Input and output is displayed as follows, I hope I could obtain your help, I will be grateful. 
Best regards
Lihui Ou
     
&CONTROL
                 calculation = 'neb' ,
                restart_mode = 'restart' ,
                      outdir = '/home/olh/tmp/' ,
                  pseudo_dir = '/home/olh/pseudo/' ,
                      prefix = 'O2-pt111-neb' ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 10.486,
                   celldm(3) = 2.979,
                         nat = 14,
                        ntyp = 2,
                     ecutwfc = 30 ,
                     ecutrho = 300 ,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.2,
   starting_magnetization(2) = 0.5,
 /
 &ELECTRONS
                    conv_thr = 1.D-6 ,
                 mixing_beta = 0.4D0 ,
             diagonalization = 'david' ,
 /
 &IONS
           pot_extrapolation = 'second_order' ,
           wfc_extrapolation = 'second_order' ,
               num_of_images = 7 ,
              first_last_opt = .TRUE. ,
                  opt_scheme = 'broyden' ,
                          ds = 2.D0 ,
                    path_thr = 0.1D0 ,
                   CI_scheme = 'no-CI' ,
                       k_max = 0.3D0 ,
                       k_min = 0.2D0 ,
 /
ATOMIC_SPECIES
   Pt  195.08000  Pt.pbe-nd-rrkjus.linux.UPF 
    O   15.99900  O.pbe-rrkjus.UPF 
ATOMIC_POSITIONS angstrom 
first_image
   Pt      2.775000000    1.602000000   -0.000000000    0  0  0 
   Pt      0.000000000    3.204000000    2.265000000    0  0  0 
   Pt      0.000000000    0.000000000    4.531000000    1  1  1 
   Pt      1.387000000    4.005000000   -0.000000000    0  0  0 
   Pt      1.387000000    0.801000000    2.265000000    0  0  0 
   Pt     -1.387000000    2.403000000    4.531000000    1  1  1 
   Pt     -1.387000000    4.005000000   -0.000000000    0  0  0 
   Pt      4.162000000    0.801000000    2.265000000    0  0  0 
   Pt      1.387000000    2.403000000    4.531000000    1  1  1 
   Pt      0.000000000    1.602000000   -0.000000000    0  0  0 
   Pt      2.775000000    3.204000000    2.265000000    0  0  0 
   Pt      2.775000000    0.000000000    4.531000000    1  1  1 
    O     -1.568000000    5.705000000    6.038000000    1  1  1 
    O     -2.597000000    6.329000000    6.038000000    1  1  1 
last_image
   Pt      2.775000000    1.602000000    0.000000000 
   Pt      0.000000000    3.204000000    2.265000000 
   Pt     -0.002257201   -0.048721794    4.608777825 
   Pt      1.387000000    4.005000000    0.000000000 
   Pt      1.387000000    0.801000000    2.265000000 
   Pt     -1.424771788    2.424931516    4.610565786 
   Pt     -1.387000000    4.005000000    0.000000000 
   Pt      4.162000000    0.801000000    2.265000000 
   Pt      1.431853343    2.425582129    4.608249503 
   Pt      0.000000000    1.602000000    0.000000000 
   Pt      2.775000000    3.204000000    2.265000000 
   Pt      2.778070234   -0.001329244    4.662167816 
    O     -0.004849711    4.796675419    6.523769755 
    O     -2.769036356    6.404956681    5.835361556 
K_POINTS automatic 
  4 4 1   1 1 1 
 
Program PWSCF     v.3.2.3  starts ...
     Today is 19Dec2007 at  1:42:29 
     Parallel version (MPI)
     Number of processors in use:       4
     R & G space division:  proc/pool =    4
     Ultrasoft (Vanderbilt) Pseudopotentials
     Current dimensions of program pwscf are:
     ntypx = 10   npk = 40000  lmax =  3
     nchix =  6  ndmx =  2000  nbrx = 14  nqfx =  8
     reading file O2-pt111-neb.path

     calculation                   =  neb
     restart_mode                  =  restart
     opt_scheme                    =  broyden
     num_of_images                 =  7
     nstep                         =  50
     CI_scheme                     =  no-CI
     first_last_opt                =  T
     coarse-grained phase-space    =  F
     use_freezing                  =  F
     ds                            =  2.0000 a.u.
     k_max                         =  0.3000 a.u.
     k_min                         =  0.2000 a.u.
     suggested k_max               =  0.1542 a.u.
     suggested k_min               =  0.1028 a.u.
     path_thr                      =  0.1000 eV / A
     ------------------------------ iteration   9 ----------------------
     tcpu =      0.1    self-consistency for image   1
     tcpu =   3995.8    self-consistency for image   2
     tcpu =   8608.3    self-consistency for image   3
     tcpu =  13585.9    self-consistency for image   4
     tcpu =  17346.0    self-consistency for image   5
     tcpu =  21022.4    self-consistency for image   6
     tcpu =  24164.4    self-consistency for image   7
     activation energy (->) =   0.032363 eV
     activation energy (<-) =   0.688354 eV
     image        energy (eV)        error (eV/A)        frozen
         1     -15003.0907527            0.994721            F
         2     -15003.0583893            1.099769            F
         3     -15003.2027444            1.212931            F
         4     -15003.3568740            0.794748            F
         5     -15003.5396707            0.224572            F
         6     -15003.6934038            0.109147            F
         7     -15003.7467437            0.010089            F
     path length          =  2.979 bohr
     inter-image distance =  0.496 bohr
     ------------------------------ iteration  10 ----------------------
     tcpu =  24626.4    self-consistency for image   1
     tcpu =  29307.7    self-consistency for image   2
     tcpu =  33298.7    self-consistency for image   3
     tcpu =  37845.1    self-consistency for image   4
     tcpu =  42086.4    self-consistency for image   5
     tcpu =  45619.3    self-consistency for image   6
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #       238
     info =/= 0
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     stopping ...
p0_3953  p4_error: : 0

 
 
 

--

======================================
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 lee0su at kist.re.kr  Wed Dec 19 13:31:07 2007
From: lee0su at kist.re.kr (lee0su at kist.re.kr)
Date: Wed, 19 Dec 2007 21:31:07 +0900 (KST)
Subject: [Pw_forum] =?euc-kr?q?Pw=5Fforum_Digest=2C_Vol_6=2C_Issue_38?=
Message-ID: <20071219123107.17E591ACA40@spam.kist.re.kr>

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From jibiaoli at gmail.com  Wed Dec 19 13:37:58 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Wed, 19 Dec 2007 20:37:58 +0800
Subject: [Pw_forum] Ni pseudopotential file
Message-ID: <b8b82da20712190437r3cb87388h2850edb94c004082@mail.gmail.com>

Dear all
Does anyone (Carlo Sbraccia or anyone else) have a Ni pp file (Ni-pbe-us.van)
generated by Carlo Sbraccia a few years ago
with the Vanderbilt code, because Carlo Sbraccia
found that the standard version available from the
PWSCF web-page had some convergency issue with respect to the plane-wave and
charge density cutoffs. I am appreciated having this pp file from Carlo
Sbraccia or someone else.

-- 
Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23925323
Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
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From njuxuyuehua at gmail.com  Wed Dec 19 13:38:30 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Wed, 19 Dec 2007 20:38:30 +0800
Subject: [Pw_forum] can these small difference between energies be
	negligible?
Message-ID: <aca2feb20712190438k28d4e266j5d53df72ab0cd71c@mail.gmail.com>

hello all here:
i am writing to ask you about the question which is motioned in my subject:
here are some  total energies(ry):calculation by pwscf,and the system has 15
atoms.
 -172.2532
-172.25322
-172.25321
-172.25321

thank you for your time.i look forward to your reply


 your sincerely

-- 
Xu Yuehua
physics Department of Nanjing university
China
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From lee0su at kist.re.kr  Wed Dec 19 08:12:04 2007
From: lee0su at kist.re.kr (lee0su at kist.re.kr)
Date: Wed, 19 Dec 2007 16:12:04 +0900 (KST)
Subject: [Pw_forum] =?euc-kr?q?Pw=5Fforum_Digest=2C_Vol_6=2C_Issue_37?=
Message-ID: <20071219071204.7962C1AC165@spam.kist.re.kr>

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From miguel.martinez at ehu.es  Wed Dec 19 14:07:53 2007
From: miguel.martinez at ehu.es (Miguel Mart=?US-ASCII?Q?=ED?=nez)
Date: Wed, 19 Dec 2007 14:07:53 +0100 (CET)
Subject: [Pw_forum] Wild phonons
Message-ID: <6425626782bcpmaczm@ehu.es>

Dear colleagues,

I've been working on high pressure phonon branches of alkali metals
lately. Having all stuff calculated with PBE, I obviously wanted an Na
PBE pseudopotential. My choice this time was Axel Kohlmeyer's
Na.pbe-nsp-van.UPF.

The thing is, at 20 GPa, even with ecutwfc=60 Ry and ecutrho=600 Ry, on
a 26 26 26 monkhorst pack grid, a change of degauss from 0.02 to 0.015
makes the low frequency mode in the [110] branch unstable. I really
can't imagine a 26 26 26 grid being too coarse for a notable jump on a
subtle smearing change. At q= 0.1 0.1 0, the results are: 

degauss = 0.02 Ry
     omega( 1) =       0.187580 [THz] =       6.257034 [cm-1]
     omega( 2) =       1.178767 [THz] =      39.319706 [cm-1]
     omega( 3) =       2.672894 [THz] =      89.158739 [cm-1]

degauss = 0.015 Ry
     omega( 1) =      -0.165534 [THz] =      -5.521640 [cm-1]
     omega( 2) =       1.183868 [THz] =      39.489864 [cm-1]
     omega( 3) =       2.673752 [THz] =      89.187356 [cm-1]

This being Na bcc at 20 GPa, having checked that its enthalpy is lower
than fcc Na with that pseudopotential, I'm worried to see such a jump in
the mode related to C'. I know that I'm close to gamma, making
convergence hard. But on the other hand, both the energy cutoff and the
k-point mesh are pretty large. 

If anybody has any comments, I'd gladly recieve them. 

By the way, is it too crazy of an idea to calculate the elastic
constants from the phonon spectrum instead of directly deformating the cell?

PS: I attach the input, in case anybody wants them:

####### Scf input:#######
 &control
    calculation='scf'
    restart_mode='from_scratch',
    tstress = .true.
    tprnfor = .true.
    prefix='na',
    pseudo_dir = '/home/wmbmacam/pseudo/',
    outdir='/scratch/wmbmacam/phon/'
 /
 &system    
    ibrav=  3, celldm(1)= 6.282 , nat=  1, ntyp= 1,
    ecutwfc = 60.0, ecutrho= 600.0
    occupations='smearing', smearing='m-p', degauss= 0.020
 /
 &electrons
    conv_thr =  1.0d-8
    mixing_beta = 0.7
 /
ATOMIC_SPECIES
 Na  22.989768  Na.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS
 Na 0.00 0.00 0.00 
K_POINTS {automatic}
 26 26 26   1 1 1


###### Nscf input #######
 &control
    calculation='phonon'
    restart_mode='from_scratch',
    prefix='na',
    pseudo_dir = '/home/wmbmacam/pseudo/',
    outdir='/scratch/wmbmacam/phon/'
 /
 &system
    ibrav=  3, celldm(1)= 6.282 , nat=  1, ntyp= 1,
    ecutwfc =60.0, ecutrho = 600.0
    occupations='smearing', smearing='m-p', degauss=0.020
 /
 &electrons
    conv_thr =  1.0d-8
 /
 &phonon
    xqq(1) = 0.10, xqq(2) = 0.10, xqq(3) = 0.00
 /
ATOMIC_SPECIES
 Na  22.989768  Na.pbe-sp-van_ak.UPF
ATOMIC_POSITIONS
 Na 0.00 0.00 0.00
K_POINTS {automatic}
 26 26 26   1 1 1

###### Phonon input ######
 &inputph
  tr2_ph=1.0d-16,
  prefix='na',
  ldisp=.false.,
  amass(1)=22.989768,
  outdir='/scratch/wmbmacam/phon/',
  fildyn='dyn.0.10,0.10,0.00',
 /
 0.10 0.10 0.00


From wlyim at puccini.che.pitt.edu  Wed Dec 19 14:04:19 2007
From: wlyim at puccini.che.pitt.edu (William Yim)
Date: Wed, 19 Dec 2007 08:04:19 -0500 (EST)
Subject: [Pw_forum] can these small difference between energies be
 negligible?
In-Reply-To: <aca2feb20712190438k28d4e266j5d53df72ab0cd71c@mail.gmail.com>
Message-ID: <Pine.LNX.4.44.0712190751110.15648-100000@puccini.che.pitt.edu>

Hi yuehua,

Your question may be oversimplified. Are you talking about the energies of 
different isomers? If yes, then I agree that the differences are 
negligible. If no, then please provide more information.

Best regards,
William 

On Wed, 19 Dec 2007, xu yuehua wrote:

> hello all here:
> i am writing to ask you about the question which is motioned in my subject:
> here are some  total energies(ry):calculation by pwscf,and the system has 15
> atoms.
>  -172.2532
> -172.25322
> -172.25321
> -172.25321
> 
> thank you for your time.i look forward to your reply
> 
> 
>  your sincerely
> 
> 

-- 
Dr. Wai-Leung Yim
Institut fuer Reine und Angewandte Chemie,
Theoretische Chemie,
Carl von Ossietzky Universtaet Oldenburg,
26129 Oldenburg,
Germany
Email: wlyim at puccini.che.pitt.edu             
Phone:	+49-441-798-3950 (office)              
Fax:	+49-441-798-3964                       


From jibiaoli at gmail.com  Wed Dec 19 14:45:38 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Wed, 19 Dec 2007 21:45:38 +0800
Subject: [Pw_forum] Problem of pseudopotential file
Message-ID: <b8b82da20712190545q7298d99dgc67fa1cf60622418@mail.gmail.com>

Dear all,
I have a Ni pp file used in calcualtions of water adsorption on Ni surfaces.
However, my calculations always stop with the following message:

  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readpp : error #         2
     inconsistent DFT read
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...


When I put a print before all line: read(iunps, *, err=100 ) as suggested by
Paolo Giannozzi, it stops with the message below:


     Program PWSCF     v.3.2.3  starts ...
     Today is 19Dec2007 at 21:15:25

     Parallel version (MPI)

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


     Ultrasoft (Vanderbilt) Pseudopotentials

     Current dimensions of program pwscf are:

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

    ============================================================

    |  pseudopotential report for atomic species:  1           |
    |        pseudo potential version   7   3   4              |
    ------------------------------------------------------------
    |  Ni (US s-loc)
28.000PZ                   exchange-corr  |
    |  z =  10.    zv( 1) =   5.    exfact =   0.00000         |
    |  ifpcor =  1           atomic energy = -95.38553 Ry      |
    |  index    orbital      occupation    energy              |

    |    1        320           8.00       -0.65               |
    |    2        400           2.00       -0.41               |
    |    3        410           0.00       -0.09               |
    |  rinner =
1.2000  1.2000  1.2000  1.2000  1.2000        |
    |    new generation scheme:                                |
    |    nbeta =  3     kkbeta =  677     rcloc =    2.0160    |
    |    ibeta    l     epsilon   rcut                         |

    |      1       1      -0.09   2.23                         |
    |      2       2      -0.65   2.00                         |
    |      3       2      -0.09   2.00                         |
    ============================================================


 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from readpp : error #         2
     inconsistent DFT read
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%


     stopping ...



The pp file is shown as following


    7    3    4   12    3 2004
Ni (US s-loc) 28.000000000 10.000000000 5.000000000
    3  939 -9.53855345677E+01
  320    8.000000000   -0.652240294
  400    2.000000000   -0.414755227
  410    0.000000000   -0.090035867
    3    1    1.200000000
    3    0 -0.41475    3    8 10.00000
  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00  1.20000000000E+00
  1.20000000000E+00
    2
  2.03000000000E+00  2.22802202189E+00  2.00000000000E+00
    3  677
    1
 -9.00366252122E-02  0.00000000000E+00 -7.19962583407E-13 -2.92845340520E-12
 -6.70053286789E-12 -1.21142191010E-11 -1.92505951636E-11 -2.81939199977E-11
 -3.90317432609E-11 -5.18550241718E-11 -6.67582545070E-11 -8.38395858919E-11
 -1.03200961533E-10 -1.24948252542E-10 -1.49191399020E-10 -1.76044556043E-10
 -2.05626244746E-10 -2.38059508658E-10 -2.73472075477E-10 -3.11996524474E-10
 -3.53770459710E-10 -3.98936689284E-10 -4.47643410790E-10 -5.00044403227E-10
 -5.56299225561E-10 -6.16573422177E-10 -6.81038735456E-10 -7.49873325718E-10
 -8.23261998791E-10 -9.01396441454E-10 -9.84475465037E-10 -1.07270525746E-09
 -1.16629964395E-09 -1.26548035688E-09 -1.37047731477E-09 -1.48152891111E-09
 -1.59888231303E-09 -1.72279377036E-09 -1.85352893531E-09 -1.99136319326E-09
 -2.13658200485E-09 -2.28948126000E-09 -2.45036764401E-09 -2.61955901643E-09
 -2.79738480282E-09 -2.98418640016E-09 -3.18031759613E-09 -3.38614500285E-09
 -3.60204850558E-09 -3.82842172686E-09 -4.06567250656E-09 -4.31422339853E-09
 -4.57451218430E-09 -4.84699240439E-09 -5.13213390798E-09 -5.43042342138E-09
 -5.74236513612E-09 -6.06848131716E-09 -6.40931293203E-09 -6.76542030159E-09
 -7.13738377308E-09 -7.52580441632E-09 -7.93130474377E-09 -8.35452945530E-09
 -8.79614620850E-09 -9.25684641545E-09 -9.73734606672E-09 -1.02383865837E-08


-- 
Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23925323
Email: jibiaoli at imr.ac.cn or jibiaoli at gmail.com
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From giannozz at nest.sns.it  Wed Dec 19 14:50:07 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 19 Dec 2007 14:50:07 +0100
Subject: [Pw_forum] Problem of pseudopotential file
In-Reply-To: <b8b82da20712190545q7298d99dgc67fa1cf60622418@mail.gmail.com>
References: <b8b82da20712190545q7298d99dgc67fa1cf60622418@mail.gmail.com>
Message-ID: <E0C56298-0D81-4CB8-AB92-CD6528E48D32@nest.sns.it>


On Dec 19, 2007, at 14:45 , Clark Lee wrote:

>      from readpp : error #         2
>      inconsistent DFT read

http://www.quantum-espresso.org/wiki/index.php/Troubleshooting_% 
28PWscf%29#pw.x_stops_with_.27inconsistent_DFT.27_error
---
Paolo Giannozzi, Dept of Physics, University of Udine
via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222




From njuxuyuehua at gmail.com  Wed Dec 19 14:59:56 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Wed, 19 Dec 2007 21:59:56 +0800
Subject: [Pw_forum] can these small difference between energies be
	negligible?
In-Reply-To: <Pine.LNX.4.44.0712190751110.15648-100000@puccini.che.pitt.edu>
References: <aca2feb20712190438k28d4e266j5d53df72ab0cd71c@mail.gmail.com>
	<Pine.LNX.4.44.0712190751110.15648-100000@puccini.che.pitt.edu>
Message-ID: <aca2feb20712190559i69d40487wbc831a41773f5f91@mail.gmail.com>

dear  all:
sorry ,i should have stated my question clearly.
in fact .i am searching the best structure via varying the crystal
lattice,these energies obtained at different crystal lattice .
from this point ,maybe it can be belong to the isomer.but  i am not sure .
thank you for your time.  i would  be grateful if you could give me some
advice .
Yours sincerely
                     yuehua


2007/12/19, William Yim <wlyim at puccini.che.pitt.edu>:
>
> Hi yuehua,
>
> Your question may be oversimplified. Are you talking about the energies of
> different isomers? If yes, then I agree that the differences are
> negligible. If no, then please provide more information.
>
> Best regards,
> William
>
> On Wed, 19 Dec 2007, xu yuehua wrote:
>
> > hello all here:
> > i am writing to ask you about the question which is motioned in my
> subject:
> > here are some  total energies(ry):calculation by pwscf,and the system
> has 15
> > atoms.
> >  -172.2532
> > -172.25322
> > -172.25321
> > -172.25321
> >
> > thank you for your time.i look forward to your reply
> >
> >
> >  your sincerely
> >
> >
>
> --
> Dr. Wai-Leung Yim
> Institut fuer Reine und Angewandte Chemie,
> Theoretische Chemie,
> Carl von Ossietzky Universtaet Oldenburg,
> 26129 Oldenburg,
> Germany
> Email: wlyim at puccini.che.pitt.edu
> Phone:  +49-441-798-3950 (office)
> Fax:    +49-441-798-3964
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>



-- 
Xu Yuehua
physics Department of Nanjing university
China
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From lee0su at kist.re.kr  Wed Dec 19 15:39:14 2007
From: lee0su at kist.re.kr (lee0su at kist.re.kr)
Date: Wed, 19 Dec 2007 23:39:14 +0900 (KST)
Subject: [Pw_forum] =?euc-kr?q?Pw=5Fforum_Digest=2C_Vol_6=2C_Issue_39?=
Message-ID: <20071219143914.E1D0D1AD260@spam.kist.re.kr>

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From marzari at MIT.EDU  Wed Dec 19 15:51:57 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 19 Dec 2007 09:51:57 -0500
Subject: [Pw_forum] Wild phonons
In-Reply-To: <6425626782bcpmaczm@ehu.es>
References: <6425626782bcpmaczm@ehu.es>
Message-ID: <4769300D.5030606@mit.edu>



Dear Miguel,

is the q=0.1 0.1 0 the result of a direct phonon calculation,
or the result of an interpolation ? If it's a matdyn interpolation,
I wouldn't be surprised at all - small changes at q=0 can really affect
your interpolation.

If it's a direct calculation, my only comment would be that a change 
from 0.02 to 0.15 is not that small (with smearing, you should think
at the inverse - i.e. it's much easier to converge with respect to
k-points when you have 0.02, that when you have 0.01).

This doesn't really solve your problems, of course, and the only thing
you need to figure out is if 26x26x26 and 0.02 is good, or not - and
the only way is to increase the k-point, and making sure htat things do
not change, and then decreasing the smearing, and retesting (painful).

I've seen samplings as high as 40x40x40 to get the elastic constants
right in Nb, from the sound velocities.

My experience is that it is less expensive to get elastic constants
from the energy than form the phonons, but once you really ramp up
the k-points (as said, even 40x40x40, and you are converged with the
smearing - not too small, not too large) the results are the same.

Note that at finite pressure one might need to be careful about
energy and enthalpy and what is exactly that you are calculating -
my guess is that you need the second derivatives of the enthalpy, and I
suspect that is what the phonon slopes would be, but it would be better
to check carefully the literature. Anyone care to comment ?

			nicola



Miguel Mart?nez wrote:
> Dear colleagues,
> 
> I've been working on high pressure phonon branches of alkali metals
> lately. Having all stuff calculated with PBE, I obviously wanted an Na
> PBE pseudopotential. My choice this time was Axel Kohlmeyer's
> Na.pbe-nsp-van.UPF.
> 
> The thing is, at 20 GPa, even with ecutwfc=60 Ry and ecutrho=600 Ry, on
> a 26 26 26 monkhorst pack grid, a change of degauss from 0.02 to 0.015
> makes the low frequency mode in the [110] branch unstable. I really
> can't imagine a 26 26 26 grid being too coarse for a notable jump on a
> subtle smearing change. At q= 0.1 0.1 0, the results are: 
> 
> degauss = 0.02 Ry
>      omega( 1) =       0.187580 [THz] =       6.257034 [cm-1]
>      omega( 2) =       1.178767 [THz] =      39.319706 [cm-1]
>      omega( 3) =       2.672894 [THz] =      89.158739 [cm-1]
> 
> degauss = 0.015 Ry
>      omega( 1) =      -0.165534 [THz] =      -5.521640 [cm-1]
>      omega( 2) =       1.183868 [THz] =      39.489864 [cm-1]
>      omega( 3) =       2.673752 [THz] =      89.187356 [cm-1]
> 
> This being Na bcc at 20 GPa, having checked that its enthalpy is lower
> than fcc Na with that pseudopotential, I'm worried to see such a jump in
> the mode related to C'. I know that I'm close to gamma, making
> convergence hard. But on the other hand, both the energy cutoff and the
> k-point mesh are pretty large. 
> 
> If anybody has any comments, I'd gladly recieve them. 
> 
> By the way, is it too crazy of an idea to calculate the elastic
> constants from the phonon spectrum instead of directly deformating the cell?

-- 
---------------------------------------------------------------------
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 marzari at MIT.EDU  Wed Dec 19 15:53:42 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Wed, 19 Dec 2007 09:53:42 -0500
Subject: [Pw_forum] Pw_forum Digest, Vol 6, Issue 39
In-Reply-To: <20071219143914.E1D0D1AD260@spam.kist.re.kr>
References: <20071219143914.E1D0D1AD260@spam.kist.re.kr>
Message-ID: <47693076.7050508@mit.edu>



Dear all,

I believe the message below needs to be answered by the
account pw_forum at pwscf.org - in order for lee0su to be
able to receive emails from the mailing list.
We see more and more of these spam filters.

				nicola


lee0su at kist.re.kr wrote:
>     	 	 	 	 	
> 					
> 					
> 				
> 		?? ?????.
> ?? *lee0su at kist.re.kr* ????? ??? ???
> ??? ??? ????? ?? ? ??? ??? ????, ?? ???? 
> ??? ??? ????, ??? ????? ??? ??? ? ????. ? 
> ?? ?? ?? ???? ????,? ? ???? ??? ????? ?????
> ? ??? ??????? ?? ???????. ??? ? ??? ??, ? 
> ?? ?????, ?? ?? ??? ?, ??? ?? ??? ?? ??? ? 
> ? ??? ?? ??? ????? ????. 		
> 	  
> <http://spam.kist.re.kr/mmpmgr/user/auth_view.php?msgid=476912910A3B&lang=kr> 
> 	  	
> 				
> 			  		
> 					
> 		??: 14? ??? ????? ???? ?? ??, ??? ??? ??? 
> ??, ? ?? ?? ?, ? ????? ??? ??? ????. 		
> 					
> 			  		
> 					
> 		This is *lee0su at kist.re.kr*.
> Please complete the verification so that I can receive your email.
> ?After finishing this verification, you can be in my address book 
> forever and won't need to do it again.?
> This is the confirmation e-mail for blocking spam e-mail. If this isn't 
> e-mail for you after checking the e-mail title, sender's e-mail address 
> and body, don't finish the confirmation process. 		
> 	  
> <http://spam.kist.re.kr/mmpmgr/user/auth_view.php?msgid=476912910A3B&lang=en> 
> 	  	
> 				
> 			  		
> 					
> 		Warning: you must confirm to deliver the mail, or it will be droped on 
> the 14th day! 		
> 					
> 		  			
> <http://nurivision.co.kr>
> 
> 
> ------------------------------------------------------------------------
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From giannozz at nest.sns.it  Wed Dec 19 16:03:35 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 19 Dec 2007 16:03:35 +0100
Subject: [Pw_forum] Pw_forum Digest, Vol 6, Issue 39
In-Reply-To: <47693076.7050508@mit.edu>
References: <20071219143914.E1D0D1AD260@spam.kist.re.kr>
	<47693076.7050508@mit.edu>
Message-ID: <07EEC4C8-962D-4BA7-8677-7940BBB64D2C@nest.sns.it>

On Dec 19, 2007, at 15:53 , Nicola Marzari wrote:

> We see more and more of these spam filters.

...that turn out to be as annoying as spam itself

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 akohlmey at cmm.chem.upenn.edu  Wed Dec 19 16:06:19 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 19 Dec 2007 10:06:19 -0500 (EST)
Subject: [Pw_forum] Pw_forum Digest, Vol 6, Issue 39
In-Reply-To: <47693076.7050508@mit.edu>
References: <20071219143914.E1D0D1AD260@spam.kist.re.kr>
	<47693076.7050508@mit.edu>
Message-ID: <Pine.LNX.4.64.0712191000260.2632@localhost.localdomain>

On Wed, 19 Dec 2007, Nicola Marzari wrote:

dear nicola,

sorry, but i'd rather recommend to unsubscribe
the account from the list and suggest using a
yahoo, hotmail, gmail, or equivalent account
for receiving mail from the mailing list instead.

otherwise this would force the mailing list 
administrator(s) to do a lot of manual work and
encourage the use of these methods that only
work well for personal mail and otherwise irritate
people a lot.

regards,
   axel.


NM> 
NM> 
NM> Dear all,
NM> 
NM> I believe the message below needs to be answered by the
NM> account pw_forum at pwscf.org - in order for lee0su to be
NM> able to receive emails from the mailing list.
NM> We see more and more of these spam filters.
NM> 
NM> 				nicola
NM> 
NM> 
NM> lee0su at kist.re.kr wrote:
NM> >     	 	 	 	 	
NM> > 					
NM> > 					
NM> > 				
NM> > 		???? ??????????.
NM> > ???? *lee0su at kist.re.kr* ?????????? ?????? ??????
NM> > ?????? ?????? ?????????? ???? ?? ?????? ?????? ????????, ???? ???????? 
NM> > ?????? ?????? ????????, ?????? ?????????? ?????? ?????? ?? ????????. ?? 
NM> > ???? ???? ???? ???????? ????????,?? ?? ???????? ?????? ?????????? ??????????
NM> > ?? ?????? ?????????????? ???? ??????????????. ?????? ?? ?????? ????, ?? 
NM> > ???? ??????????, ???? ???? ?????? ??, ?????? ???? ?????? ???? ?????? ?? 
NM> > ?? ?????? ???? ?????? ?????????? ????????. 		
NM> > 	  
NM> > <http://spam.kist.re.kr/mmpmgr/user/auth_view.php?msgid=476912910A3B&lang=kr> 
NM> > 	  	
NM> > 				
NM> > 			  		
NM> > 					
NM> > 		????: 14?? ?????? ?????????? ???????? ???? ????, ?????? ?????? ?????? 
NM> > ????, ?? ???? ???? ??, ?? ?????????? ?????? ?????? ????????. 		
NM> > 					
NM> > 			  		
NM> > 					
NM> > 		This is *lee0su at kist.re.kr*.
NM> > Please complete the verification so that I can receive your email.
NM> > ??After finishing this verification, you can be in my address book 
NM> > forever and won't need to do it again.??
NM> > This is the confirmation e-mail for blocking spam e-mail. If this isn't 
NM> > e-mail for you after checking the e-mail title, sender's e-mail address 
NM> > and body, don't finish the confirmation process. 		
NM> > 	  
NM> > <http://spam.kist.re.kr/mmpmgr/user/auth_view.php?msgid=476912910A3B&lang=en> 
NM> > 	  	
NM> > 				
NM> > 			  		
NM> > 					
NM> > 		Warning: you must confirm to deliver the mail, or it will be droped on 
NM> > the 14th day! 		
NM> > 					
NM> > 		  			
NM> > <http://nurivision.co.kr>
NM> > 
NM> > 
NM> > ------------------------------------------------------------------------
NM> > 
NM> > _______________________________________________
NM> > Pw_forum mailing list
NM> > Pw_forum at pwscf.org
NM> > http://www.democritos.it/mailman/listinfo/pw_forum
NM> 
NM> 
NM> 

-- 
=======================================================================
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 tone.kokalj at ijs.si  Wed Dec 19 17:53:49 2007
From: tone.kokalj at ijs.si (Tone Kokalj)
Date: Wed, 19 Dec 2007 17:53:49 +0100
Subject: [Pw_forum] About NEB restart
In-Reply-To: <23594730.634771198067403681.JavaMail.coremail@bj126app103.126.com>
References: <23594730.634771198067403681.JavaMail.coremail@bj126app103.126.com>
Message-ID: <1198083229.2600.61.camel@localhost.localdomain>


On Wed, 2007-12-19 at 20:30 +0800, oulihui666 wrote:
> Dear pwscf users,
>     Recently, I encounter a problem about neb, I intend to calculate
> the neb about adsorption, unfortunately, power cut, so I want to
> restart the calculation following interrupted task by using 'restart',
> but when I restart the calculation, error information is displayed.  
> ...
>      inter-image distance =  0.496 bohr
>      ------------------------------ iteration  10
> ----------------------
>      tcpu =  24626.4    self-consistency for image   1
>      tcpu =  29307.7    self-consistency for image   2
>      tcpu =  33298.7    self-consistency for image   3
>      tcpu =  37845.1    self-consistency for image   4
>      tcpu =  42086.4    self-consistency for image   5
>      tcpu =  45619.3    self-consistency for image   6
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%
>      from cdiaghg : error #       238
>      info =/= 0
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> %%
>      stopping ...
> p0_3953  p4_error: : 0

The calculation crashed in image 6; clean the outdir/prefix_6 directory, and restart the calculation.

In your particular case that would be: rm -rf /home/olh/tmp/O2-pt111-neb_6/*

Regards, Tone Kokalj
-- 
J. Stefan Institute, Ljubljana, Slovenia



From miguel.martinez at ehu.es  Wed Dec 19 18:40:52 2007
From: miguel.martinez at ehu.es (=?ISO-8859-1?Q?Miguel_Marti=ADnez?=)
Date: Wed, 19 Dec 2007 18:40:52 +0100
Subject: [Pw_forum] Wild phonons
In-Reply-To: <4769300D.5030606@mit.edu>
References: <6425626782bcpmaczm@ehu.es> <4769300D.5030606@mit.edu>
Message-ID: <476957A4.7040608@ehu.es>

Dear Nicola,

Thank you very much for your answer. One of the things that puzzled me is 
that k-point convergence was way easier on the NC LDA pseudopotential 
available on the web. Or at least it seemed that way. I always thought that 
including semicore states would only incur in a cutoff "penalty", so to 
speak. Or maybe the semicore states are more sensitive to changes only 
properly descrived in a fine mesh.

Finally, I'd like to apologise everybody for not including my affiliation 
in the signature when using the webmail client.

Regards,

Miguel

PS: Calculating elastic constants at finite pressure does indeed require 
knowledge of what one is doing, especially since nearly every single 
textbook assumes zero presssure in its derivations.

Nicola Marzari escribi?:
> 
> Dear Miguel,
> 
> is the q=0.1 0.1 0 the result of a direct phonon calculation,
> or the result of an interpolation ? If it's a matdyn interpolation,
> I wouldn't be surprised at all - small changes at q=0 can really affect
> your interpolation.
> 
> If it's a direct calculation, my only comment would be that a change 
> from 0.02 to 0.15 is not that small (with smearing, you should think
> at the inverse - i.e. it's much easier to converge with respect to
> k-points when you have 0.02, that when you have 0.01).
> 
> This doesn't really solve your problems, of course, and the only thing
> you need to figure out is if 26x26x26 and 0.02 is good, or not - and
> the only way is to increase the k-point, and making sure htat things do
> not change, and then decreasing the smearing, and retesting (painful).
> 
> I've seen samplings as high as 40x40x40 to get the elastic constants
> right in Nb, from the sound velocities.
> 
> My experience is that it is less expensive to get elastic constants
> from the energy than form the phonons, but once you really ramp up
> the k-points (as said, even 40x40x40, and you are converged with the
> smearing - not too small, not too large) the results are the same.
> 
> Note that at finite pressure one might need to be careful about
> energy and enthalpy and what is exactly that you are calculating -
> my guess is that you need the second derivatives of the enthalpy, and I
> suspect that is what the phonon slopes would be, but it would be better
> to check carefully the literature. Anyone care to comment ?
> 

-- 
----------------------------------------
Miguel Mart?nez Canales
    Dto. F?sica de la Materia Condensada
    UPV/EHU
    Facultad de Ciencia y Tecnolog?a
    Apdo. 644
    48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 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 nest.sns.it  Wed Dec 19 19:02:49 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 19 Dec 2007 19:02:49 +0100
Subject: [Pw_forum] Wild phonons
In-Reply-To: <4769300D.5030606@mit.edu>
References: <6425626782bcpmaczm@ehu.es> <4769300D.5030606@mit.edu>
Message-ID: <AA7673AA-BECD-4567-82CC-903C50C51C3C@nest.sns.it>


On Dec 19, 2007, at 15:51 , Nicola Marzari wrote:

> Note that at finite pressure one might need to be careful about
> energy and enthalpy and what is exactly that you are calculating -
> my guess is that you need the second derivatives of the enthalpy,  
> and I
> suspect that is what the phonon slopes would be, but it would be  
> better
> to check carefully the literature. Anyone care to comment ?

this is what I understood years ago when I wrote some lecture notes
mentioning this aspect: http://www.fisica.uniud.it/~giannozz/Corsi/ 
sissa02.pdf
see pages 20 and 21, and the reference quoted at the end:
PRL 78, 2493 (1993)

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 wangzhentang at gmail.com  Thu Dec 20 07:19:25 2007
From: wangzhentang at gmail.com (zhentang wang)
Date: Thu, 20 Dec 2007 14:19:25 +0800
Subject: [Pw_forum] relax question
In-Reply-To: <4a46d6b10712192213r46e02271rd1ad3ff20dc78d65@mail.gmail.com>
References: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com>
	<4768E08F.20204@sissa.it>
	<4a46d6b10712190636g77bceb44nef04fbc1c495225a@mail.gmail.com>
	<4a46d6b10712192213r46e02271rd1ad3ff20dc78d65@mail.gmail.com>
Message-ID: <4a46d6b10712192219x14182712ne8ed2c49cc32f921@mail.gmail.com>

Dear stefano

Thank for you answer ,but I check that the  atomic configuration by use of
xcrysden and  find non atoms overlap. But when I use one cpu instead of
parallel   conculation ,there is no problem (ecutwfc=60,ecutrho=300.0. ).
Besides  ecutwfc = ?should be reasonable for Mn.

parallel   conculation error information is displayed
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     from cdiaghg : error #       686
     info =/= 0
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

     stopping ...
rank 0 in job 21  node02_37027   caused collective abort of all ranks
  exit status of rank 0: killed by signal 9




Thank you very much!
Best  regards
zhentangwang

2007/12/20, zhentang wang <wangzhentang at gmail.com>:
>
> Dear stefano
>
> Thank for you answer ,but I check that the  atomic configuration by use
> of  xcrysden and  find non atoms overlap. But when I use one cpu instead
> of   parallel   conculation ,there is no problem (ecutwfc=60,ecutrho=300.0.
> ).
> Besides  ecutwfc = ?should be reasonable for Mn.
>
> parallel   conculation error information is displayed
> %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      from cdiaghg : error #       686
>      info =/= 0
>
>  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>
>      stopping ...
> rank 0 in job 21  node02_37027   caused collective abort of all ranks
>   exit status of rank 0: killed by signal 9
>
>
>
>
> Thank you very much!
> Best  regards
> zhentangwang
>
> 2007/12/19, zhentang wang < wangzhentang at gmail.com>:
> >
> > Dear stefano
> >
> > Thank for you answer ,but I check that the  atomic configuration by use
> > of  xcrysden and  find non atoms overlap. But when I use one cpu instead
> > of   parallel   conculation ,there is no problem (ecutwfc=60,ecutrho=
> > 300.0. ).
> > Besides  ecutwfc = ?should be reasonable for Mn.
> >
> > parallel   conculation error information is displayed
> > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >      from cdiaghg : error #       686
> >      info =/= 0
> >
> >  %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> >
> >      stopping ...
> > rank 0 in job 21  node02_37027   caused collective abort of all ranks
> >   exit status of rank 0: killed by signal 9
> >
> >
> >
> >
> > Thank you very much!
> > Best  regards
> > zhentangwang
> > 2007/12/19, Stefano de Gironcoli < degironc at sissa.it>:
> > >
> > > the first error is related to a scf calculation that did not
> > > converged...this may be due to various causes. have you checked that
> > > the
> > > atomic configuration is reasonable and non atoms overlap ?
> > > the second error is an error in diagonalization ... it means that your
> > > hamiltonian is probably corrupted or very strange ... have you checked
> > >
> > > that the atomic configuration is reasonable and non atoms overlap ?
> > > 22 + 100 Ry should be reasonable for Ga and As but  are probably  too
> > > small for Mn
> > >
> > > stefano
> > >
> > >
> > > zhentang wang wrote:
> > > > Dear pwscf users,
> > > >
> > > > I  am runing in  parallel a relax conculation ,and there are some
> > > > problems to ask.
> > > >
> > > > cluster  Set up
> > > >
> > > > pwscf  versin:      3.2.3
> > > >
> > > >  compiler:             ifort     I_fc_p_10.0.23     mkl9.1.023
> > > >
> > > > mpi:                       moich2-1.0.06
> > > > system :                cluster xeon 5345 (64bit)
> > > >
> > > > Input
> > > > &control
> > > >     calculation='relax',
> > > >     restart_mode='from_scratch',
> > > >     prefix='GaMnAs',
> > > >     pseudo_dir = '/home/ztwang/PP',
> > > >     outdir='tmp',
> > > >     tprnfor=.true.,
> > > >     disk_io='high',
> > > >     verbosity='high',
> > > > /
> > > >  &system
> > > >     ibrav=1, celldm(1) = 21.0,
> > > >     nat=65, ntyp=3,
> > > >     ecutwfc=60,
> > > >     ecutrho=360.0,
> > > >     starting_magnetization(1)=0.3,
> > > >     starting_magnetization(2)= 0.0,
> > > >     nspin=2,
> > > >     occupations='smearing',
> > > >     degauss=0.02,
> > > >     smearing='cold',
> > > > /
> > > > &electrons
> > > >      mixing_beta = 0.5
> > > >      conv_thr =   1.0d-6
> > > >      mixing_mode='local-TF'
> > > > /
> > > > &ions
> > > > //
> > > > ATOMIC_SPECIES
> > > >   Mn   54.938049  MnPZus_15e.vdb.DB.UPF
> > > >  Ga    69.723    Ga.pz-bhs.UPF
> > > >  As   74.92160    As.pz-bhs.UPF
> > > > ATOMIC_POSITIONS
> > > > Mn      0.250000000     0.250000000      0.250000000
> > > > Ga      0.000000000     0.000000000      0.000000000
> > > > Ga      0.000000000      0.250000000      0.250000000
> > > > Ga      0.250000000     0.000000000      0.250000000
> > > > Ga      0.250000000     0.250000000      0.000000000
> > > > As      0.125000000     0.125000000      0.125000000
> > > > As      0.125000000      0.375000000       0.375000000
> > > > As      0.375000000     0.125000000      0.375000000
> > > > As      0.375000000     0.375000000      0.125000000
> > > > Ga      0.000000000     0.000000000      0.500000000
> > > > Ga      0.000000000       0.250000000      0.750000000
> > > > Ga      0.250000000     0.000000000      0.750000000
> > > > Ga      0.250000000     0.250000000      0.500000000
> > > > As      0.125000000     0.125000000      0.625000000
> > > > As      0.125000000      0.375000000      0.875000000
> > > > As      0.375000000     0.125000000      0.875000000
> > > > As      0.375000000     0.375000000      0.625000000
> > > > Ga      0.000000000     0.500000000       0.000000000
> > > > Ga      0.000000000      0.750000000      0.250000000
> > > > Ga      0.250000000     0.500000000      0.250000000
> > > > Ga      0.250000000     0.750000000      0.000000000
> > > > As      0.125000000      0.625000000      0.125000000
> > > > As      0.125000000      0.875000000      0.375000000
> > > > As      0.375000000     0.625000000      0.375000000
> > > > As      0.375000000     0.875000000      0.125000000
> > > > Ga      0.000000000     0.500000000      0.500000000
> > > > Ga      0.000000000      0.750000000      0.750000000
> > > > Ga      0.250000000     0.500000000      0.750000000
> > > > Ga      0.250000000     0.750000000       0.500000000
> > > > As      0.125000000     0.625000000      0.625000000
> > > > As      0.125000000      0.875000000      0.875000000
> > > > As      0.375000000     0.625000000      0.875000000
> > > > As      0.375000000      0.875000000      0.625000000
> > > > Ga      0.500000000     0.000000000      0.000000000
> > > > Ga      0.500000000      0.250000000      0.250000000
> > > > Ga      0.750000000     0.000000000      0.250000000
> > > > Ga      0.750000000     0.250000000      0.000000000
> > > > As      0.625000000     0.125000000      0.125000000
> > > > As      0.625000000      0.375000000      0.375000000
> > > > As      0.875000000     0.125000000       0.375000000
> > > > As      0.875000000     0.375000000      0.125000000
> > > > Ga      0.500000000     0.000000000      0.500000000
> > > > Ga      0.500000000      0.250000000      0.750000000
> > > > Ga      0.750000000      0.000000000      0.750000000
> > > > Ga      0.750000000     0.250000000      0.500000000
> > > > As      0.625000000     0.125000000      0.625000000
> > > > As      0.625000000      0.375000000      0.875000000
> > > > As      0.875000000     0.125000000      0.875000000
> > > > As      0.875000000     0.375000000      0.625000000
> > > > Ga      0.500000000     0.500000000      0.000000000
> > > > Ga      0.500000000      0.750000000       0.250000000
> > > > Ga      0.750000000     0.500000000      0.250000000
> > > > Ga      0.750000000     0.750000000      0.000000000
> > > > As      0.625000000     0.625000000      0.125000000
> > > > As      0.625000000       0.875000000      0.375000000
> > > > As      0.875000000     0.625000000      0.375000000
> > > > As      0.875000000     0.875000000      0.125000000
> > > > Ga      0.500000000     0.500000000      0.500000000
> > > > Ga      0.500000000      0.750000000      0.750000000
> > > > Ga      0.750000000     0.500000000      0.750000000
> > > > Ga      0.750000000     0.750000000      0.500000000
> > > > As      0.625000000     0.625000000       0.625000000
> > > > As      0.625000000      0.875000000      0.875000000
> > > > As      0.875000000     0.625000000      0.875000000
> > > > As      0.875000000     0.875000000      0.625000000
> > > > K_POINTS {automatic}
> > > > 2 2 2 1 1 1
> > > >
> > > > error information was found, it displyed
> > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > > > End of self-consistent calculation
> > > > convergence NOT achieved, stopping
> > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > > >
> > > > And then I  change ecutwfc=40,ecutrho=200.0
> > > > error information was found, it displyed
> > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > > > %%%%%%%%%%%%%%%%%%%%%%%%%%
> > > >      from cdiaghg : error #       679
> > > >      info =/= 0
> > > > %%%%%%%%%%%%%%%%%%%%%%%%%%%
> > > >
> > > >      stopping ...
> > > > rank 0 in job 16  node01_33013   caused collective abort of all
> > > ranks
> > > >   exit status of rank 0: killed by signal 9
> > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> > > > And then I  change ecutwfc=22,ecutrho= 100.0,there is also no
> > > > problem.but I think total energy may be not  accurate.
> > > > I  wonder if this is a problem with the system or a problem of the
> > > > grogram(MPI) or a problem with input setting.
> > > >
> > > >
> > > >
> > > >
> > > > Thank you very much in advance,
> > > >
> > > > Best  regards
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > >
> > > ------------------------------------------------------------------------
> > > >
> > > > _______________________________________________
> > > > Pw_forum mailing list
> > > > Pw_forum at pwscf.org
> > > > http://www.democritos.it/mailman/listinfo/pw_forum
> > > >
> > >
> > > _______________________________________________
> > > Pw_forum mailing list
> > > Pw_forum at pwscf.org
> > > http://www.democritos.it/mailman/listinfo/pw_forum
> > >
> >
> >
> >
>
>
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From miguel.martinez at ehu.es  Thu Dec 20 09:57:07 2007
From: miguel.martinez at ehu.es (=?ISO-8859-1?Q?Miguel_Marti=ADnez?=)
Date: Thu, 20 Dec 2007 09:57:07 +0100
Subject: [Pw_forum] relax question
In-Reply-To: <4a46d6b10712192219x14182712ne8ed2c49cc32f921@mail.gmail.com>
References: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com><47	68E08F.20204@sissa.it><4a46d6b10712190636g77bceb44nef04fbc1c495225a@mail.gm	ail.com><4a46d6b10712192213r46e02271rd1ad3ff20dc78d65@mail.gmail.com>
	<4a46d6b10712192219x14182712ne8ed2c49cc32f921@mail.gmail.com>
Message-ID: <476A2E63.1090406@ehu.es>

Dear Zhentang wang,

zhentang wang escribi?:
> Besides  ecutwfc = ? should be reasonable for Mn.

Although 60 Ry looks reasonable, I don't really know. However, as ecutwfc 
is more-or-less system independent, you can take a simple Mn system (let's 
say fcc Mn with celldm(1)~14 bohr, no need to use the full I-43m structure) 
and check convergence.


-- 
----------------------------------------
Miguel Mart?nez Canales
    Dto. F?sica de la Materia Condensada
    UPV/EHU
    Facultad de Ciencia y Tecnolog?a
    Apdo. 644
    48080 Bilbao (Spain)
Fax:  +34 94 601 3500
Tlf:  +34 94 601 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 nest.sns.it  Thu Dec 20 12:42:27 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 20 Dec 2007 12:42:27 +0100
Subject: [Pw_forum] relax question
In-Reply-To: <476A2E63.1090406@ehu.es>
References: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com><47	68E08F.20204@sissa.it><4a46d6b10712190636g77bceb44nef04fbc1c495225a@mail.gm	ail.com><4a46d6b10712192213r46e02271rd1ad3ff20dc78d65@mail.gmail.com>
	<4a46d6b10712192219x14182712ne8ed2c49cc32f921@mail.gmail.com>
	<476A2E63.1090406@ehu.es>
Message-ID: <F06A2C5F-79AC-4771-90EC-075CC4CEB371@nest.sns.it>


On Dec 20, 2007, at 9:57 , Miguel Marti nez wrote:

> Although 60 Ry looks reasonable, I don't really know.
> However, as ecutwfc is more-or-less system independent,
> you can take a simple Mn system (let's say fcc Mn with
> celldm(1)~14 bohr, no need to use the full I-43m structure)
> and check convergence.

convergence should be perfect with ecutwfc=55Ry, quite
reasonable with ecutwfc=35Ry and ecutrho=300Ry.
Coming back to the original problem:
- there are two paragraphs in the user guide, in section
  "troubleshooting", for self-consistency problems and
   for the "cdiaghg error" problem
- it is very unlikely that the latter is a bug of the code
- mathematical libraries are sometimes a source of
   trouble: please try to replace mkl with internal
   blas/lapack or with atlas
- the cvs version uses a different (and hoperfully better)
   distributed-matrix parallelization algorithm
By the way: I seriously doubt that LDA is the good choice
for Mn-doped GaAs

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 wangzhentang at gmail.com  Thu Dec 20 14:13:11 2007
From: wangzhentang at gmail.com (zhentang wang)
Date: Thu, 20 Dec 2007 21:13:11 +0800
Subject: [Pw_forum] relax question
In-Reply-To: <F06A2C5F-79AC-4771-90EC-075CC4CEB371@nest.sns.it>
References: <4a46d6b10712181932m29537b16r8bc94bd13d005049@mail.gmail.com>
	<4a46d6b10712192213r46e02271rd1ad3ff20dc78d65@mail.gmail.com>
	<4a46d6b10712192219x14182712ne8ed2c49cc32f921@mail.gmail.com>
	<476A2E63.1090406@ehu.es>
	<F06A2C5F-79AC-4771-90EC-075CC4CEB371@nest.sns.it>
Message-ID: <4a46d6b10712200513y61c7d16fva07d570234fc7924@mail.gmail.com>

Dear Paolo and Miguel
I will try.
Thanks for your reply.


zhentangwang
2007/12/20, Paolo Giannozzi <giannozz at nest.sns.it>:
>
>
> On Dec 20, 2007, at 9:57 , Miguel Marti nez wrote:
>
> > Although 60 Ry looks reasonable, I don't really know.
> > However, as ecutwfc is more-or-less system independent,
> > you can take a simple Mn system (let's say fcc Mn with
> > celldm(1)~14 bohr, no need to use the full I-43m structure)
> > and check convergence.
>
> convergence should be perfect with ecutwfc=55Ry, quite
> reasonable with ecutwfc=35Ry and ecutrho=300Ry.
> Coming back to the original problem:
> - there are two paragraphs in the user guide, in section
>   "troubleshooting", for self-consistency problems and
>    for the "cdiaghg error" problem
> - it is very unlikely that the latter is a bug of the code
> - mathematical libraries are sometimes a source of
>    trouble: please try to replace mkl with internal
>    blas/lapack or with atlas
> - the cvs version uses a different (and hoperfully better)
>    distributed-matrix parallelization algorithm
> By the way: I seriously doubt that LDA is the good choice
> for Mn-doped GaAs
>
> 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 ierrea001 at ikasle.ehu.es  Thu Dec 20 15:42:32 2007
From: ierrea001 at ikasle.ehu.es (Ion Errea)
Date: Thu, 20 Dec 2007 15:42:32 +0100
Subject: [Pw_forum] electron-phonon coefficients
Message-ID: <1198161752.9917.35.camel@localhost>

Dear PWscf users,

Lately I am trying to calculate a rough estimation of the
superconducting transition temperature of a Li-Be alloy under pressure.
For that goal, I calculated using the espresso code the electron-phonon
coupling constant, lambda, and the Eliashberg function, a2F. Thus I
should be able to calculate Tc via the McMillan equation.

I am writing a simple fortran program to calculate the average phonon
frequency, involved in the McMillan equation, from a integration of the
values obtained for a2F in the output. Nevertheless, I got a result that
I did not expect at all for the average phonon frequency. To check the
reliability of my naive program, I calculated lambda from the a2F values
as well. Curiously, I obtained a lambda 2pi times the lambda given in
the output. Checking the theory I realised that there is a 2pi factor
dividing in the Eliashberg function. 

I am just wondering whether this 2pi factor is implemented in the a2F
output, or it is incorporated afterwards when lambda is calculated. I
guess the latter is the correct answer since such casualities are not
too common. Anyway, my program could perfectly be wrong. I would be very
grateful if someone would confirm my supposition.

Regards,

Ion

-- 
========================================
Ion Errea Lope
Materia Kondentsatuaren Fisika Saila
Zientzia eta Teknologia Fakultatea
Euskal Herriko Unibertsitatea 
644 Posta Kutxatila, 48080 Bilbo, Spain

Telefonoa: +34 946015322
Mail: ierrea001 at ikasle.ehu.es
========================================



From chenhanghuipwscf at gmail.com  Thu Dec 20 17:53:46 2007
From: chenhanghuipwscf at gmail.com (alan chen)
Date: Thu, 20 Dec 2007 11:53:46 -0500
Subject: [Pw_forum] mixing_beta and mixing_ndim
Message-ID: <22ae3ca40712200853j23204493nb83b6b85912adcc5@mail.gmail.com>

Dear PWSCF users,
      I have a question about 'mixing_beta' and 'mixing_ndim'.  In one 'scf'
calculations, I found it converges very slowly.  The 'estimated scf
accuracy'  remains almost a constant in the two subsequent iterations.  Do
you think whether it will help if I change 'mixing_beta' or 'mixing_ndim',
making them larger or smaller?
      Thank you.


Hanghui Chen
Department of Physics, Yale University
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From degironc at sissa.it  Thu Dec 20 18:12:58 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Thu, 20 Dec 2007 18:12:58 +0100
Subject: [Pw_forum] mixing_beta and mixing_ndim
In-Reply-To: <22ae3ca40712200853j23204493nb83b6b85912adcc5@mail.gmail.com>
References: <22ae3ca40712200853j23204493nb83b6b85912adcc5@mail.gmail.com>
Message-ID: <476AA29A.1070407@sissa.it>

I think there is no general strategy.
you can try increasing  mixing_ndim and/or reducing mixing_beta.
Another possibility is to change mixing_mode from "plane" (the default) 
to TF or local-TF.
This should help in the case the instability is due to charge sloshing 
(large metallic systems)...
A source of instability can be that from one iteration to the next the 
list of occupied level
changes... increasing number of bands, number of k-points and/or 
smearing width may help.
If your system use gradient corrected functionals and has a lot of 
vacuum there may be some
problem related to spurious negative charge that can be  possibly solved 
by increasing ecutrho....
It is difficult to give a general advise...
Stefano de Gironcoli,

> Dear PWSCF users,
>       I have a question about 'mixing_beta' and 'mixing_ndim'.  In one 
> 'scf' calculations, I found it converges very slowly.  The 'estimated 
> scf accuracy'  remains almost a constant in the two subsequent 
> iterations.  Do you think whether it will help if I change 
> 'mixing_beta' or 'mixing_ndim', making them larger or smaller?
>       Thank you.
>     
>
> Hanghui Chen
> Department of Physics, Yale University
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From a.mostofi at imperial.ac.uk  Thu Dec 20 19:47:27 2007
From: a.mostofi at imperial.ac.uk (Arash Mostofi)
Date: Thu, 20 Dec 2007 18:47:27 +0000
Subject: [Pw_forum] Wannier90 v1.1
Message-ID: <476AB8BF.2040001@imperial.ac.uk>

Dear PW users

Version 1.1 of the Wannier90 code is now available at 
http://www.wannier.org. Wannier90 is a tool for obtaining 
maximally-localised Wannier functions and using them to calculate a wide 
range of electronic properties. The code is seamlessly interfaced to 
PWSCF. See http://www.wannier.org for more details.

Cheers

Arash Mostofi

-- 
:------------------------------------------------------------:
: Dr. Arash A. Mostofi           :: a.mostofi at imperial.ac.uk :
: Lecturer and RCUK Fellow       ::                          :
: Depts. of Materials & Physics  ::                          :
: Imperial College London        :: T  +44 (0)207 594 6753   :
: London SW7 2AZ, United Kingdom :: F  +44 (0)207 594 6757   :
:------- http://www.cmth.ph.ic.ac.uk/people/a.mostofi -------:

From hqzhou at nju.edu.cn  Fri Dec 21 04:39:39 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 21 Dec 2007 11:39:39 +0800
Subject: [Pw_forum] About ecutwfc and ecutrho again
Message-ID: <004b01c84383$1da02370$1d00a8c0@solarflare>

Dear PWscfers,

I'm creating and testing pseudopotentials for severval
elements myself. I plotted the E-ecutwfc graphs for 
each element, in which the ecutwfc was ranging from 20
to 60 with increament of 5 Ry and ecutrho was set to 600.
If take 1 mRy as convergence criterion, I find that the
total energy for some elements will be convergent at
ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.

If the material I'm interested in is comprised from elements
with both lower and higher ecutwfc, what ecutwfc should I
set for the material, the higher one, the higher one plus
alpha, or a compromise between the lower and higher?

Thnaks!


Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China  

 





From marzari at MIT.EDU  Fri Dec 21 05:52:56 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 20 Dec 2007 23:52:56 -0500
Subject: [Pw_forum] About ecutwfc and ecutrho again
In-Reply-To: <004b01c84383$1da02370$1d00a8c0@solarflare>
References: <004b01c84383$1da02370$1d00a8c0@solarflare>
Message-ID: <476B46A8.7060704@mit.edu>



Roughly speaking, the higher ecutwfc among the elements
considered.

Are these ultrasoft or norm conserving ? If the latter,
ecutrho could have been safely kept to 240 Ry.

If the former, my rule of thumb is that rarely a cutoff
greater than 30 Ry is needed, unless subtle magnetic/spin
propertes are sought. Thi sis to say that absolute convergence of
the energy is not the most useful criterion - often one looks
at lattice parameter, bulk modulus, or phonon frequencies as
good indicators of convergence.

				nicola

Huiqun Zhou wrote:
> Dear PWscfers,
> 
> I'm creating and testing pseudopotentials for severval
> elements myself. I plotted the E-ecutwfc graphs for 
> each element, in which the ecutwfc was ranging from 20
> to 60 with increament of 5 Ry and ecutrho was set to 600.
> If take 1 mRy as convergence criterion, I find that the
> total energy for some elements will be convergent at
> ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.
> 
> If the material I'm interested in is comprised from elements
> with both lower and higher ecutwfc, what ecutwfc should I
> set for the material, the higher one, the higher one plus
> alpha, or a compromise between the lower and higher?
> 
> Thnaks!
> 
> 
> Dr. Huiqun Zhou
> @Earth Sciences, Nanjing University, China  


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From baroni at sissa.it  Fri Dec 21 08:03:36 2007
From: baroni at sissa.it (Stefano Baroni)
Date: Fri, 21 Dec 2007 08:03:36 +0100
Subject: [Pw_forum] About ecutwfc and ecutrho again
In-Reply-To: <004b01c84383$1da02370$1d00a8c0@solarflare>
References: <004b01c84383$1da02370$1d00a8c0@solarflare>
Message-ID: <0FC6F0EE-F1B1-4CDE-BFEF-EDC1917DFD74@sissa.it>

the largest - as a home assignment, please take half an hour to think  
about this and provide us with an explanation. SB

On Dec 21, 2007, at 4:39 AM, Huiqun Zhou wrote:

> Dear PWscfers,
>
> I'm creating and testing pseudopotentials for severval
> elements myself. I plotted the E-ecutwfc graphs for
> each element, in which the ecutwfc was ranging from 20
> to 60 with increament of 5 Ry and ecutrho was set to 600.
> If take 1 mRy as convergence criterion, I find that the
> total energy for some elements will be convergent at
> ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.
>
> If the material I'm interested in is comprised from elements
> with both lower and higher ecutwfc, what ecutwfc should I
> set for the material, the higher one, the higher one plus
> alpha, or a compromise between the lower and higher?
>
> Thnaks!
>
>
> Dr. Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
>
>
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum

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

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



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From hqzhou at nju.edu.cn  Fri Dec 21 13:08:20 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 21 Dec 2007 20:08:20 +0800
Subject: [Pw_forum] About ecutwfc and ecutrho again
References: <004b01c84383$1da02370$1d00a8c0@solarflare>
	<476B46A8.7060704@mit.edu>
Message-ID: <012b01c843ca$2dd1fb50$1d00a8c0@solarflare>

Thanks, Nicola and Stefano,

Actually, I was thinking the choice should be the lagest or lagest plus 
alpha.
The pseudopotentials I'm testing are USPP for iron, chromium, oxygen and
others, and one of the materials I'm interested is chromite (FeCr2O4). I 
found
ecutwfc for iron and chromium is indeed around 35 Ry for convergence, but
over 55 Ry for oxygen. I haven't checked whether I did anything wrong when
creating potential for oxygen, but it's consistent with the results of 
convergence
test for chromite, in which ecutwfc should be set to 55 Ry (ecutrho=600) for
convergence.

Please comment.


Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China


----- Original Message ----- 
From: "Nicola Marzari" <marzari at MIT.EDU>
To: "PWSCF Forum" <pw_forum at pwscf.org>
Sent: Friday, December 21, 2007 12:52 PM
Subject: Re: [Pw_forum] About ecutwfc and ecutrho again


>
>
> Roughly speaking, the higher ecutwfc among the elements
> considered.
>
> Are these ultrasoft or norm conserving ? If the latter,
> ecutrho could have been safely kept to 240 Ry.
>
> If the former, my rule of thumb is that rarely a cutoff
> greater than 30 Ry is needed, unless subtle magnetic/spin
> propertes are sought. Thi sis to say that absolute convergence of
> the energy is not the most useful criterion - often one looks
> at lattice parameter, bulk modulus, or phonon frequencies as
> good indicators of convergence.
>
> nicola
>
> Huiqun Zhou wrote:
>> Dear PWscfers,
>>
>> I'm creating and testing pseudopotentials for severval
>> elements myself. I plotted the E-ecutwfc graphs for
>> each element, in which the ecutwfc was ranging from 20
>> to 60 with increament of 5 Ry and ecutrho was set to 600.
>> If take 1 mRy as convergence criterion, I find that the
>> total energy for some elements will be convergent at
>> ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.
>>
>> If the material I'm interested in is comprised from elements
>> with both lower and higher ecutwfc, what ecutwfc should I
>> set for the material, the higher one, the higher one plus
>> alpha, or a compromise between the lower and higher?
>>
>> Thnaks!
>>
>>
>> Dr. Huiqun Zhou
>> @Earth Sciences, Nanjing University, China
>
>
> -- 
> ---------------------------------------------------------------------
> 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
> 


From akohlmey at cmm.chem.upenn.edu  Fri Dec 21 13:16:20 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Fri, 21 Dec 2007 13:16:20 +0100
Subject: [Pw_forum] About ecutwfc and ecutrho again
In-Reply-To: <012b01c843ca$2dd1fb50$1d00a8c0@solarflare>
References: <004b01c84383$1da02370$1d00a8c0@solarflare>
	<476B46A8.7060704@mit.edu> <012b01c843ca$2dd1fb50$1d00a8c0@solarflare>
Message-ID: <7b6913e90712210416t60988b1dje1f060ee7dde7685@mail.gmail.com>

On 12/21/07, Huiqun Zhou <hqzhou at nju.edu.cn> wrote:

> Thanks, Nicola and Stefano,
>
> Actually, I was thinking the choice should be the lagest or lagest plus
> alpha.
> The pseudopotentials I'm testing are USPP for iron, chromium, oxygen and
> others, and one of the materials I'm interested is chromite (FeCr2O4). I
> found
> ecutwfc for iron and chromium is indeed around 35 Ry for convergence, but
> over 55 Ry for oxygen. I haven't checked whether I did anything wrong when
> creating potential for oxygen, but it's consistent with the results of
> convergence

if you are using the "bm" vanderbilt oxygen potentials, those were created
with a wavefunction cutoff of 25 to 35 rydberg in mind.

> test for chromite, in which ecutwfc should be set to 55 Ry (ecutrho=600) for
> convergence.
>
> Please comment.

as was already noted. the convergence of the total energy is much
slower as other properties (e.g. forces). so you can get an accurate result
for geometry optimization with much smaller cutoffs for both wavefunction
and density.

to test this, you can build a (distorted) geometry and monitor forces
and/or stress tensor etc. pp.

cheers,
    axel.





>
>
> Dr. Huiqun Zhou
> @Earth Sciences, Nanjing University, China
>
>
> ----- Original Message -----
> From: "Nicola Marzari" <marzari at MIT.EDU>
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Sent: Friday, December 21, 2007 12:52 PM
> Subject: Re: [Pw_forum] About ecutwfc and ecutrho again
>
>
> >
> >
> > Roughly speaking, the higher ecutwfc among the elements
> > considered.
> >
> > Are these ultrasoft or norm conserving ? If the latter,
> > ecutrho could have been safely kept to 240 Ry.
> >
> > If the former, my rule of thumb is that rarely a cutoff
> > greater than 30 Ry is needed, unless subtle magnetic/spin
> > propertes are sought. Thi sis to say that absolute convergence of
> > the energy is not the most useful criterion - often one looks
> > at lattice parameter, bulk modulus, or phonon frequencies as
> > good indicators of convergence.
> >
> > nicola
> >
> > Huiqun Zhou wrote:
> >> Dear PWscfers,
> >>
> >> I'm creating and testing pseudopotentials for severval
> >> elements myself. I plotted the E-ecutwfc graphs for
> >> each element, in which the ecutwfc was ranging from 20
> >> to 60 with increament of 5 Ry and ecutrho was set to 600.
> >> If take 1 mRy as convergence criterion, I find that the
> >> total energy for some elements will be convergent at
> >> ecutwfc = 35 Ry while some are around ecutwfc = 55 Ry.
> >>
> >> If the material I'm interested in is comprised from elements
> >> with both lower and higher ecutwfc, what ecutwfc should I
> >> set for the material, the higher one, the higher one plus
> >> alpha, or a compromise between the lower and higher?
> >>
> >> Thnaks!
> >>
> >>
> >> Dr. Huiqun Zhou
> >> @Earth Sciences, Nanjing University, China
> >
> >
> > --
> > ---------------------------------------------------------------------
> > 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
> >
>
> _______________________________________________
> 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 eyvaz_isaev at yahoo.com  Fri Dec 21 14:06:02 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Fri, 21 Dec 2007 05:06:02 -0800 (PST)
Subject: [Pw_forum] Merry X-mass!
In-Reply-To: <0FC6F0EE-F1B1-4CDE-BFEF-EDC1917DFD74@sissa.it>
Message-ID: <940887.68374.qm@web60317.mail.yahoo.com>

Dear all, 

Well, it is time to start for X-Mass celebration.
So, Merry X-mass and Happy New Year!

My best wishies for developers and, of course, users.

Eyvaz.  

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


      ____________________________________________________________________________________
Looking for last minute shopping deals?  
Find them fast with Yahoo! Search.  http://tools.search.yahoo.com/newsearch/category.php?category=shopping

From lanhaiping at gmail.com  Fri Dec 21 14:17:27 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Fri, 21 Dec 2007 21:17:27 +0800
Subject: [Pw_forum] Merry X-mass!
In-Reply-To: <940887.68374.qm@web60317.mail.yahoo.com>
References: <0FC6F0EE-F1B1-4CDE-BFEF-EDC1917DFD74@sissa.it>
	<940887.68374.qm@web60317.mail.yahoo.com>
Message-ID: <c92002fa0712210517l498d390pd656fcfc30ea6767@mail.gmail.com>

Thank you !
Merry X-Mass, and Happy new year !
Wish you all have a wonderful  holiday  .

Bests,

Hai-Ping

On Dec 21, 2007 9:06 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:

> Dear all,
>
> Well, it is time to start for X-Mass celebration.
> So, Merry X-mass and Happy New Year!
>
> My best wishies for developers and, of course, users.
>
> Eyvaz.
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys,
> Russia, and
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com
>
>
>
>  ____________________________________________________________________________________
> Looking for last minute shopping deals?
> Find them fast with Yahoo! Search.
> http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> _______________________________________________
> 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 njuxuyuehua at gmail.com  Fri Dec 21 15:27:26 2007
From: njuxuyuehua at gmail.com (xu yuehua)
Date: Fri, 21 Dec 2007 22:27:26 +0800
Subject: [Pw_forum] Merry X-mass!
In-Reply-To: <c92002fa0712210517l498d390pd656fcfc30ea6767@mail.gmail.com>
References: <0FC6F0EE-F1B1-4CDE-BFEF-EDC1917DFD74@sissa.it>
	<940887.68374.qm@web60317.mail.yahoo.com>
	<c92002fa0712210517l498d390pd656fcfc30ea6767@mail.gmail.com>
Message-ID: <aca2feb20712210627h77cce35aucec36db2522f2d4a@mail.gmail.com>

best wishes to all !
and i hope that  the  forum would  be a better place to learn pwscf  and
exchange ideas next year!




2007/12/21, lan haiping <lanhaiping at gmail.com>:
>
> Thank you !
> Merry X-Mass, and Happy new year !
> Wish you all have a wonderful  holiday  .
>
> Bests,
>
> Hai-Ping
>
> On Dec 21, 2007 9:06 PM, Eyvaz Isaev < eyvaz_isaev at yahoo.com> wrote:
>
> > Dear all,
> >
> > Well, it is time to start for X-Mass celebration.
> > So, Merry X-mass and Happy New Year!
> >
> > My best wishies for developers and, of course, users.
> >
> > Eyvaz.
> >
> > -------------------------------------------------------------------
> > Prof. Eyvaz Isaev,
> > Theoretical Physics Department, Moscow State Institute of Steel &
> > Alloys, Russia, and
> > Condensed Matter Theory Group, Uppsala University, Sweden
> > Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com
> >
> >
> >
> >  ____________________________________________________________________________________
> > Looking for last minute shopping deals?
> > Find them fast with Yahoo! Search.
> > http://tools.search.yahoo.com/newsearch/category.php?category=shopping
> > _______________________________________________
> > 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
>
>


-- 
Xu Yuehua
physics Department of Nanjing university
China
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From marzari at MIT.EDU  Fri Dec 21 15:57:54 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Fri, 21 Dec 2007 09:57:54 -0500
Subject: [Pw_forum] About ecutwfc and ecutrho again
In-Reply-To: <7b6913e90712210416t60988b1dje1f060ee7dde7685@mail.gmail.com>
References: <004b01c84383$1da02370$1d00a8c0@solarflare>	<476B46A8.7060704@mit.edu>
	<012b01c843ca$2dd1fb50$1d00a8c0@solarflare>
	<7b6913e90712210416t60988b1dje1f060ee7dde7685@mail.gmail.com>
Message-ID: <476BD472.2080001@mit.edu>

Axel Kohlmeyer wrote:

> if you are using the "bm" vanderbilt oxygen potentials, those were created
> with a wavefunction cutoff of 25 to 35 rydberg in mind.


By the way, that O gave us odd results in water - we tested it
together with  a norm conserving, an O rrkj, and also compared with
Galli's results. All pseudos were giving the same numbers, a part
from the bm O:

http://www.pwscf.org/pseudo/upfdetails.php?upf=O.pbe-van_bm.UPF

				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 szs_naghavi at yahoo.com  Sat Dec 22 09:06:30 2007
From: szs_naghavi at yahoo.com (zahra sadat naghavi)
Date: Sat, 22 Dec 2007 00:06:30 -0800 (PST)
Subject: [Pw_forum] phonon dispersion curve
Message-ID: <950380.26025.qm@web63015.mail.re1.yahoo.com>

dear anybody!
  with zonefolding approximation there must be 6*(n+1)  branches in phonon dispersion curve for achiral  nanotubes , for (6,6)  it becomes 42, but i found  45 frequencies at G.
  what is the wrong?

       
---------------------------------
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From kazempoor2000 at yahoo.com  Sat Dec 22 13:44:46 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Sat, 22 Dec 2007 04:44:46 -0800 (PST)
Subject: [Pw_forum] average.x
Message-ID: <917959.80911.qm@web33102.mail.mud.yahoo.com>

Dear all
what is the input file for average.x?can i average
potential from the lateral facet of nanotube or
nanowire?
thanks


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From degironc at sissa.it  Sat Dec 22 14:49:50 2007
From: degironc at sissa.it (Stefano de Gironcoli)
Date: Sat, 22 Dec 2007 14:49:50 +0100
Subject: [Pw_forum] phonon dispersion curve
In-Reply-To: <950380.26025.qm@web63015.mail.re1.yahoo.com>
References: <950380.26025.qm@web63015.mail.re1.yahoo.com>
Message-ID: <476D15FE.2030907@sissa.it>

In any system with nat atoms per unit cell  there are 3*nat frequencies 
at any q-vector in the BZ since there are 3*nat independent 
displacements that can be performed.
stefano

zahra sadat naghavi wrote:
> dear anybody!
> with zonefolding approximation there must be 6*(n+1)  branches in 
> phonon dispersion curve for achiral  nanotubes , for (6,6)  it becomes 
> 42, but i found  45 frequencies at G.
> what is the wrong?
>
> ------------------------------------------------------------------------
> Be a better friend, newshound, and know-it-all with Yahoo! Mobile. Try 
> it now. 
> <http://us.rd.yahoo.com/evt=51733/*http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ%20> 
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>   


From giannozz at nest.sns.it  Fri Dec 21 18:34:59 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 21 Dec 2007 18:34:59 +0100
Subject: [Pw_forum] average.x
In-Reply-To: <917959.80911.qm@web33102.mail.mud.yahoo.com>
References: <917959.80911.qm@web33102.mail.mud.yahoo.com>
Message-ID: <200712211834.59774.giannozz@nest.sns.it>

On Saturday 22 December 2007 13:44, ali kazempoor wrote:

> what is the input file for average.x?

it is described in the header of file average.f90

Paolo
--
Paolo Giannozzi, Democritos and University of Udine

From meisam_a84 at yahoo.com  Sun Dec 23 09:23:30 2007
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Sun, 23 Dec 2007 00:23:30 -0800 (PST)
Subject: [Pw_forum] optimizing pw input parameters
Message-ID: <286763.84392.qm@web30605.mail.mud.yahoo.com>

Dear all
which parameters should be optimized sequencly in a scf runing? the parameters are celldm(1),ecutwfc, ecutrho,mixing-beta and K-points.
another problem is that for optimizing the ecutwfc the system converges for some numbers and it doesn't for some more. I have to mention that there is overlap in davidson diagonalization.


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From mbaris at metu.edu.tr  Sun Dec 23 12:50:24 2007
From: mbaris at metu.edu.tr (mbaris at metu.edu.tr)
Date: Sun, 23 Dec 2007 13:50:24 +0200
Subject: [Pw_forum] optimizing pw input parameters
In-Reply-To: <20071223111859.49pukis6rs748okk@webmail2.metu.edu.tr>
References: <20071223111859.49pukis6rs748okk@webmail2.metu.edu.tr>
Message-ID: <20071223135024.ovanwl5p7ogg88g0@webmail2.metu.edu.tr>

Dear Meisam Aghtar,

> which parameters should be optimized sequencly in a scf runing? the 
> parameters are celldm(1),ecutwfc, ecutrho,mixing-beta and K-points.

All of them.

> another problem is that for optimizing the ecutwfc the system 
> converges for some numbers and it doesn't for some more. I have to 
> mention that there is overlap in davidson diagonalization.
>

yes, they have such bad manners.




As previously mentioned in the forum, observables such as celldm(1) 
converge much more rapidly than total energy. I do not know about your 
specific problem, but what I do for in the project I am currently 
working on is this: I have written a small script that scans a given 
parameter range (ecutwfc, ecutrho, etc) and minimizes celldm(1) for the 
specific set using a golden search algorithm, then, plotting the 
results (for example celldm(1) vs ecutwfc for different k-point sets), 
I decide which set to use.

why do you want to alter mixing beta? Do you have convergence problems?

and for ecutrho, it is generally safe to use 10xecutwfc,  (remember, I 
do not know what you are working on, and assuming something 
straightforward). Please dig more about how ecutrho is used in the 
code.  and it is better to add your affiliation after a post.

Merry X-mas everyone!

Osman Baris Malcioglu
Ph.D. Candidate
METU Physics
Ankara, Turkey








From oulihui666 at 126.com  Mon Dec 24 03:47:42 2007
From: oulihui666 at 126.com (oulihui666)
Date: Mon, 24 Dec 2007 10:47:42 +0800 (CST)
Subject: [Pw_forum] About nelec and tot_charge again
Message-ID: <29982528.607331198464462921.JavaMail.coremail@bj126app81.126.com>

Dear pwscf users,   
    I have asked the similar problem last time, but I do not understand this 
problem very explicitly. I want to do a structural relaxation of a charged 
system using pwscf. For example, In the process of oxygen reduction reaction, 
adsorption of hydration proton(H3O+) on Pt(111) surface,  simultaneously, a 
extra electron is added, that is to say, O2 + H+ + e- . When I calculate this 
system with pwscf, could I add charge and add a electron simultanously? My input 
file is displayed as follows, In this system, there is 157 electrons, when I add 
a extra electron, it is 158 electron, simultanously, I add +1 charge, when I run 
input file, I do not get an error information, is this correct? I need your 
help.   
Thanks in advance     
Lihui Ou   
 &CONTROL
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                      outdir = '/home/olh/tmp/' ,
                  pseudo_dir = '/home/olh/pseudo/' ,
                      prefix = 'O2-H7O3-pt111-relax' ,
                       nstep = 200 ,
                     tstress = .true. ,
                     tprnfor = .true. ,
 /
 &SYSTEM
                       ibrav = 4,
                   celldm(1) = 10.486,
                   celldm(3) = 2.979,
                         nat = 24,
                        ntyp = 3,
                     ecutwfc = 30 ,
                     ecutrho = 300 ,
                       nelec = 158,
                  tot_charge = 1.000000,
                 occupations = 'smearing' ,
                     degauss = 0.02 ,
                    smearing = 'methfessel-paxton' ,
                       nspin = 2 ,
   starting_magnetization(1) = 0.2,
   starting_magnetization(2) = 0.5,
   starting_magnetization(3) = 1.0,
 /
 &ELECTRONS
                    conv_thr = 1.D-6 ,
                 mixing_beta = 0.4D0 ,
             diagonalization = 'david' ,
 /
 &IONS
                ion_dynamics = 'bfgs' ,
 /
ATOMIC_SPECIES
   Pt  195.08000  Pt.pbe-nd-rrkjus.linux.UPF 
    O   15.99900  O.pbe-rrkjus.UPF 
    H    1.00800  H.pbe-rrkjus.linux.UPF 
ATOMIC_POSITIONS angstrom 
   Pt      2.775000000    1.602000000   -0.000000000    0  0  0 
   Pt      0.000000000    3.204000000    2.265000000    0  0  0 
   Pt      0.000000000    0.000000000    4.531000000    1  1  1 
   Pt      1.387000000    4.005000000   -0.000000000    0  0  0 
   Pt      1.387000000    0.801000000    2.265000000    0  0  0 
   Pt     -1.387000000    2.403000000    4.531000000    1  1  1 
   Pt     -1.387000000    4.005000000   -0.000000000    0  0  0 
   Pt      4.162000000    0.801000000    2.265000000    0  0  0 
   Pt      1.387000000    2.403000000    4.531000000    1  1  1 
   Pt      0.000000000    1.602000000   -0.000000000    0  0  0 
   Pt      2.775000000    3.204000000    2.265000000    0  0  0 
   Pt      2.775000000    0.000000000    4.531000000    1  1  1 
    O      1.238000000    0.876000000    6.331000000    1  1  1 
    O      0.209000000    1.500000000    6.331000000    1  1  1 
    H      1.443000000    1.185000000    9.230000000    1  1  1 
    O      0.605000000    1.362000000    8.820000000    1  1  1 
    H      0.363000000    2.268000000    8.975000000    1  1  1 
    H      0.670000000    1.207000000    7.885000000    1  1  1 
    H     -0.878000000    3.907000000   11.663000000    1  1  1 
    O     -1.128000000    3.097000000   11.233000000    1  1  1 
    H     -2.045000000    2.917000000   11.406000000    1  1  1 
    H      3.018000000    2.594000000   11.726000000    1  1  1 
    O      2.652000000    1.744000000   11.513000000    1  1  1 
    H      2.797000000    1.146000000   12.237000000    1  1  1 
K_POINTS automatic 
  4 4 1   1 1 1 


--

======================================
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 lanhaiping at gmail.com  Mon Dec 24 05:49:14 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Mon, 24 Dec 2007 12:49:14 +0800
Subject: [Pw_forum] About nelec and tot_charge again
In-Reply-To: <29982528.607331198464462921.JavaMail.coremail@bj126app81.126.com>
References: <29982528.607331198464462921.JavaMail.coremail@bj126app81.126.com>
Message-ID: <c92002fa0712232049p5497efcah3c267635a7f2ac61@mail.gmail.com>

Hi? Do you read the input document of pwscf?
it explicitly claims that  tot_charge is used only if nelec is unspecified,
and otherwise it is ignored !

On Dec 24, 2007 10:47 AM, oulihui666 <oulihui666 at 126.com> wrote:

> Dear pwscf users,
>     I have asked the similar problem last time, but I do not understand
> this
> problem very explicitly. I want to do a structural relaxation of a charged
>
> system using pwscf. For example, In the process of oxygen reduction
> reaction,
> adsorption of hydration proton(H3O+) on Pt(111) surface,  simultaneously,
> a
> extra electron is added, that is to say, O2 + H+ + e- . When I calculate
> this
> system with pwscf, could I add charge and add a electron simultanously? My
> input
> file is displayed as follows, In this system, there is 157 electrons, when
> I add
> a extra electron, it is 158 electron, simultanously, I add +1 charge, when
> I run
> input file, I do not get an error information, is this correct? I need
> your
> help.
> Thanks in advance
> Lihui Ou
>  &CONTROL
>                  calculation = 'relax' ,
>                 restart_mode = 'from_scratch' ,
>                       outdir = '/home/olh/tmp/' ,
>                   pseudo_dir = '/home/olh/pseudo/' ,
>                       prefix = 'O2-H7O3-pt111-relax' ,
>                        nstep = 200 ,
>                      tstress = .true. ,
>                      tprnfor = .true. ,
>  /
>  &SYSTEM
>                        ibrav = 4,
>                    celldm(1) = 10.486,
>                    celldm(3) = 2.979,
>                          nat = 24,
>                         ntyp = 3,
>                      ecutwfc = 30 ,
>                      ecutrho = 300 ,
>                        nelec = 158,
>                   tot_charge = 1.000000,
>                  occupations = 'smearing' ,
>                      degauss = 0.02 ,
>                     smearing = 'methfessel-paxton' ,
>                        nspin = 2 ,
>    starting_magnetization(1) = 0.2,
>    starting_magnetization(2) = 0.5,
>    starting_magnetization(3) = 1.0,
>  /
>  &ELECTRONS
>                     conv_thr = 1.D-6 ,
>                  mixing_beta = 0.4D0 ,
>              diagonalization = 'david' ,
>  /
>  &IONS
>                 ion_dynamics = 'bfgs' ,
>  /
> ATOMIC_SPECIES
>    Pt  195.08000  Pt.pbe-nd-rrkjus.linux.UPF
>     O   15.99900  O.pbe-rrkjus.UPF
>     H    1.00800  H.pbe-rrkjus.linux.UPF
> ATOMIC_POSITIONS angstrom
>    Pt      2.775000000    1.602000000   -0.000000000    0  0  0
>    Pt      0.000000000    3.204000000    2.265000000    0  0  0
>    Pt      0.000000000    0.000000000    4.531000000    1  1  1
>    Pt      1.387000000    4.005000000   -0.000000000    0  0  0
>    Pt      1.387000000    0.801000000    2.265000000    0  0  0
>    Pt     -1.387000000    2.403000000    4.531000000    1  1  1
>    Pt     -1.387000000    4.005000000   -0.000000000    0  0  0
>    Pt      4.162000000    0.801000000    2.265000000    0  0  0
>    Pt      1.387000000    2.403000000    4.531000000    1  1  1
>    Pt      0.000000000    1.602000000   -0.000000000    0  0  0
>    Pt      2.775000000    3.204000000    2.265000000    0  0  0
>    Pt      2.775000000    0.000000000    4.531000000    1  1  1
>     O      1.238000000    0.876000000    6.331000000    1  1  1
>     O      0.209000000    1.500000000    6.331000000    1  1  1
>     H      1.443000000    1.185000000    9.230000000    1  1  1
>     O      0.605000000    1.362000000    8.820000000    1  1  1
>     H      0.363000000    2.268000000    8.975000000    1  1  1
>     H      0.670000000    1.207000000    7.885000000    1  1  1
>     H     -0.878000000    3.907000000   11.663000000    1  1  1
>     O     -1.128000000    3.097000000   11.233000000    1  1  1
>     H     -2.045000000    2.917000000   11.406000000    1  1  1
>     H      3.018000000    2.594000000   11.726000000    1  1  1
>     O      2.652000000    1.744000000   11.513000000    1  1  1
>     H      2.797000000    1.146000000   12.237000000    1  1  1
> K_POINTS automatic
>   4 4 1   1 1 1
>
> --
>  ======================================
> 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*
> ======================================
>
> _______________________________________________
> 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 shrek_826 at yahoo.com.cn  Mon Dec 24 07:40:27 2007
From: shrek_826 at yahoo.com.cn (Fan Yang)
Date: Mon, 24 Dec 2007 14:40:27 +0800 (CST)
Subject: [Pw_forum] about electron charge density
Message-ID: <539880.94729.qm@web15310.mail.cnb.yahoo.com>

Dear everyone,
       Does anyone know how to plot electron charge density along a line or in a plane?  
 
======================================
Fan Yang
PH.D Candidate in Electrochemistry                      
College of Chemistry and Molecular Science            
Wuhan University,430072,Hubei Province,China 
E-mail:shrek_826 at yahoo.com.cn
======================================


      ____________________________________________________________________________________
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From paulatto at sissa.it  Mon Dec 24 11:41:54 2007
From: paulatto at sissa.it (Lorenzo Paulatto)
Date: Mon, 24 Dec 2007 11:41:54 +0100 (CET)
Subject: [Pw_forum] about electron charge density
In-Reply-To: <539880.94729.qm@web15310.mail.cnb.yahoo.com>
References: <539880.94729.qm@web15310.mail.cnb.yahoo.com>
Message-ID: <25728.82.52.171.42.1198492914.squirrel@webmail.sissa.it>


On Mon, December 24, 2007 07:40, Fan Yang wrote:
> Dear everyone,
>        Does anyone know how to plot electron charge density along a line
> or in a plane?


Dear Fan Yang,
you have to use pp.x to postprcess the charge density in order to extract
the planar density or the line density. Than you can plot it with
plotrho.x or with other software, depending on the output format you have
asked to pp.x

See example05 and INPUT_PP for more information.

Goodbye


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


----------------------------------------------------------------
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From oulihui666 at 126.com  Mon Dec 24 12:11:47 2007
From: oulihui666 at 126.com (oulihui666)
Date: Mon, 24 Dec 2007 19:11:47 +0800 (CST)
Subject: [Pw_forum] About nelec and tot_charge again
Message-ID: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>

Dear lan haiping,
  Maybe you have misunderstand my meaning, I intend to ask wheather I could add a extra electron and +1 charge simultaneously? I also have read Doc. In my systems, how should I implement this process? 
  Thank you in advance
  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 meisam_a84 at yahoo.com  Mon Dec 24 12:15:54 2007
From: meisam_a84 at yahoo.com (meisam aghtar)
Date: Mon, 24 Dec 2007 03:15:54 -0800 (PST)
Subject: [Pw_forum] optimizing pw input parameters
Message-ID: <602892.21431.qm@web30610.mail.mud.yahoo.com>

Dear Osman Baris

I'm working on zigzag carbon nanotube. my problem is that my system doesn't converg , I don't know the steps in order that the parameters should be optimized. I don't know the mixing beta should be optimized or not! I have to mention that there is overlap in Davidson diagonalization.
Meisam Aghtar
M.Sc
Physics Department of Kashan university.  


----- Original Message ----
From: "mbaris at metu.edu.tr" <mbaris at metu.edu.tr>
To: PWSCF Forum <pw_forum at pwscf.org>
Sent: Sunday, December 23, 2007 3:20:24 PM
Subject: Re: [Pw_forum] optimizing pw input parameters

Dear Meisam Aghtar,

> which parameters should be optimized sequencly in a scf runing? the 
> parameters are celldm(1),ecutwfc, ecutrho,mixing-beta and K-points.

All of them.

> another problem is that for optimizing the ecutwfc the system 
> converges for some numbers and it doesn't for some more. I have to 
> mention that there is overlap in davidson diagonalization.
>

yes, they have such bad manners.




As previously mentioned in the forum, observables such as celldm(1) 
converge much more rapidly than total energy. I do not know about your 
specific problem, but what I do for in the project I am currently 
working on is this: I have written a small script that scans a given 
parameter range (ecutwfc, ecutrho, etc) and minimizes celldm(1) for the 
specific set using a golden search algorithm, then, plotting the 
results (for example celldm(1) vs ecutwfc for different k-point sets), 
I decide which set to use.

why do you want to alter mixing beta? Do you have convergence problems?

and for ecutrho, it is generally safe to use 10xecutwfc,  (remember, I 
do not know what you are working on, and assuming something 
straightforward). Please dig more about how ecutrho is used in the 
code.  and it is better to add your affiliation after a post.

Merry X-mas everyone!

Osman Baris Malcioglu
Ph.D. Candidate
METU Physics
Ankara, Turkey







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


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From hande at newton.physics.metu.edu.tr  Mon Dec 24 12:21:31 2007
From: hande at newton.physics.metu.edu.tr (Hande Ustunel)
Date: Mon, 24 Dec 2007 13:21:31 +0200 (EET)
Subject: [Pw_forum] optimizing pw input parameters
In-Reply-To: <602892.21431.qm@web30610.mail.mud.yahoo.com>
Message-ID: <Pine.LNX.4.44.0712241317581.13014-100000@newton.physics.metu.edu.tr>

> doesn't converg , I don't know the steps in order that the parameters
> should be optimized. I don't know the mixing beta should be optimized or

Depends on what you mean by "doesn't converge". If your individual total
energy steps are fluctuating, tweaking the mxing_beta parameter might
help. If the indiviual calculations you do converge all right for a given
set of parameters you don't have to change mixing_beta.

I believe it might be beneficial for you if you learnt a little more about
the theory that goes into DFT calculations. I recommend, for example, the
book by Richard Martin or several review papers available on the arxiv and
elsewhere on the web. Meanings of some of the parameters might become more
transparent to you.

Best,
Hande


-- 
Hande Ustunel
Department of Physics
Office 439
Middle East Technical University
Ankara 06531, Turkey
Tel : +90 312 210 3264
http://www.physics.metu.edu.tr/~hande


From mbaris at metu.edu.tr  Mon Dec 24 12:27:03 2007
From: mbaris at metu.edu.tr (mbaris at metu.edu.tr)
Date: Mon, 24 Dec 2007 13:27:03 +0200
Subject: [Pw_forum] about electron charge density
In-Reply-To: <25728.82.52.171.42.1198492914.squirrel@webmail.sissa.it>
References: <539880.94729.qm@web15310.mail.cnb.yahoo.com>
	<25728.82.52.171.42.1198492914.squirrel@webmail.sissa.it>
Message-ID: <20071224132703.ls5e02ucwfs0kosk@webmail2.metu.edu.tr>

Dear Fan Yang,

Please have a look at the examples directory for more detailed use, 
here is a quick example for plotting rho along a line (v 3.2.2) :

1) Run pwscf to get the results
2) Run pp.x and prepare a datafile for rho (can be re-used) , input:

&inputPP
outdir='same_output_dir_as_your_pwscf_run',
prefix='same_prefix_as_your_pwscf_run',
filplot=???some_file_name.dat???
plot_num=0,
/

3) run pp.x again to prepare the plot along a line
input:

    &inputPP
    /
    &plot
    filepp(1)='some_file_name.dat'
    iflag=1,
    e1(1) =0.1744477,   e1(2)=-0.100708, e1(3) = 0.0228807 , (this is 
vector direction in alat coordinates)    x0(1) =-0.0077775, 
x0(2)=0.5764514, x0(3) =0.9558631 , (this is the vector origin in alat 
coordinates)
    nx=50, (number of sampling points)
    output_format=0,
    fileout=???some_other_filename_for_gnuplot.gdat???
    /


of course you can also do it in single input,

best,

Osman Baris Malcioglu
Ph.D. Candidate
METU Physics, Ankara, Turkey



From akohlmey at cmm.chem.upenn.edu  Mon Dec 24 13:48:54 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Mon, 24 Dec 2007 13:48:54 +0100
Subject: [Pw_forum] About nelec and tot_charge again
In-Reply-To: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>
References: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>
Message-ID: <7b6913e90712240448l7feaaabase64d52f5635b964f@mail.gmail.com>

On 12/24/07, oulihui666 <oulihui666 at 126.com> wrote:
> Dear lan haiping,
>   Maybe you have misunderstand my meaning, I intend to ask wheather I could
> add a extra electron and +1 charge simultaneously? I also have read Doc. In
> my systems, how should I implement this process?

please use some common sense.

adding an electron _and_ a proton is equivalent to adding
a single hydrogen _atom_ and the total charge of the system
does not change because of that. in any quantum chemistry
calculation you always specify the _total_ charge and the _total_
number of electrons and get the _total_ electron structure.
there are no labels on the electrons that tell whom they belong to,
and a positive charge is nothing but the lack of an electron.

cheers,
   axel.


>   Thank you in advance
>   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
> ======================================
> _______________________________________________
> 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 jackygrahamez at gmail.com  Mon Dec 24 18:49:29 2007
From: jackygrahamez at gmail.com (Jack Shultz)
Date: Mon, 24 Dec 2007 12:49:29 -0500
Subject: [Pw_forum] Cygwin Install Issue
Message-ID: <6c65435e0712240949p6907abbv2c5f1cbd2b70f963@mail.gmail.com>

Any idea why I get this error message?


make[1]: Entering directory `/usr/src/espresso-3.2.3/iotk'
cd src ; make libiotk.a
make[2]: Entering directory `/usr/src/espresso-3.2.3/iotk/src'
make[2]: `libiotk.a' is up to date.
make[2]: Leaving directory `/usr/src/espresso-3.2.3/iotk/src'
make[1]: Leaving directory `/usr/src/espresso-3.2.3/iotk'
( cd Modules ; if test "make" = "" ; then make  TLDEPS= all ; \
        else make  TLDEPS= all ; fi )
make[1]: Entering directory `/usr/src/espresso-3.2.3/Modules'
g95 -O3 -cpp -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./
-I../Modules  -I
../iotk/src -I../PW  -I../PH  -I../CPV -c xml_io_base.f90
In file xml_io_base.f90:17

  USE iotk_module
                 1
Fatal Error: Can't open module file 'iotk_module.mod' at (1) for reading: No
suc
h file or directory
make[1]: *** [xml_io_base.o] Error 1
make[1]: Leaving directory `/usr/src/espresso-3.2.3/Modules'
make: *** [mods] Error 2
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From jackygrahamez at gmail.com  Mon Dec 24 20:15:26 2007
From: jackygrahamez at gmail.com (Jack Shultz)
Date: Mon, 24 Dec 2007 14:15:26 -0500
Subject: [Pw_forum] Cygwin Install Issue
In-Reply-To: <6c65435e0712240949p6907abbv2c5f1cbd2b70f963@mail.gmail.com>
References: <6c65435e0712240949p6907abbv2c5f1cbd2b70f963@mail.gmail.com>
Message-ID: <6c65435e0712241115m2bacaf62ie004fc9f74aeeb6e@mail.gmail.com>

Disregard, I think the issue was I lost my internet connection on my initial
download.

On 12/24/07, Jack Shultz <jackygrahamez at gmail.com> wrote:
>
> Any idea why I get this error message?
>
>
> make[1]: Entering directory `/usr/src/espresso-3.2.3/iotk'
> cd src ; make libiotk.a
> make[2]: Entering directory `/usr/src/espresso-3.2.3/iotk/src'
> make[2]: `libiotk.a' is up to date.
> make[2]: Leaving directory `/usr/src/espresso- 3.2.3/iotk/src'
> make[1]: Leaving directory `/usr/src/espresso-3.2.3/iotk'
> ( cd Modules ; if test "make" = "" ; then make  TLDEPS= all ; \
>         else make  TLDEPS= all ; fi )
> make[1]: Entering directory `/usr/src/espresso- 3.2.3/Modules'
> g95 -O3 -cpp -D__FFTW -D__USE_INTERNAL_FFTW -I../include  -I./
> -I../Modules  -I
> ../iotk/src -I../PW  -I../PH  -I../CPV -c xml_io_base.f90
> In file xml_io_base.f90:17
>
>   USE iotk_module
>                  1
> Fatal Error: Can't open module file 'iotk_module.mod' at (1) for reading:
> No suc
> h file or directory
> make[1]: *** [xml_io_base.o] Error 1
> make[1]: Leaving directory `/usr/src/espresso- 3.2.3/Modules'
> make: *** [mods] Error 2
>
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From lanhaiping at gmail.com  Tue Dec 25 06:23:23 2007
From: lanhaiping at gmail.com (lan haiping)
Date: Tue, 25 Dec 2007 13:23:23 +0800
Subject: [Pw_forum] About nelec and tot_charge again
In-Reply-To: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>
References: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>
Message-ID: <c92002fa0712242123jf8e526eh3ae5e38259e0c2bd@mail.gmail.com>

As far i know, you can not achieve this goal in the periodic condition
scheme.

On Dec 24, 2007 7:11 PM, oulihui666 <oulihui666 at 126.com> wrote:

> Dear lan haiping,
>   Maybe you have misunderstand my meaning, I intend to ask wheather
> I could add a extra electron and +1 charge simultaneously? I also have read
> Doc. In my systems, how should I implement this process?
>   Thank you in advance
>   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*
> ======================================
>
> _______________________________________________
> 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 gaoguoying at gmail.com  Tue Dec 25 09:55:14 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Tue, 25 Dec 2007 16:55:14 +0800
Subject: [Pw_forum] the unit of lambda
Message-ID: <6234c0c60712250055g62b126c4t881dd77e8ee64334@mail.gmail.com>

Dear pwscf users,

         I have done electron-phonon coupling calculations for a
period. However, a question confused me for a long time, that is,
there is
no unit for the electron pnonon coupling parameter lambda. Does anyone
know the reason for this? Any help will be appreciated.

Merry Christmas!

Guoying

From oulihui666 at 126.com  Tue Dec 25 10:09:17 2007
From: oulihui666 at 126.com (oulihui666)
Date: Tue, 25 Dec 2007 17:09:17 +0800 (CST)
Subject: [Pw_forum] About relaxation and cpmd
Message-ID: <13859583.505811198573757266.JavaMail.coremail@bj126app103.126.com>

Dear all,
    I have a naive problem, and need your help. I have not understanded this problem 
for a long time, etc. the difference between relaxation and molecular dynamics(cpmd), I 
think that there is many steps in the process of relaxation, and every step denotes 
a intermediate, however, It also contains many intermediate in molecular dynamics 
simulation, I do not understand the difference between relxation and molecular 
dynamics(cpmd) at all times. Anyone who would give suggestion will be appreciated.
    Thanks in advance
    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 eyvaz_isaev at yahoo.com  Tue Dec 25 11:53:13 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Tue, 25 Dec 2007 02:53:13 -0800 (PST)
Subject: [Pw_forum] the unit of lambda
In-Reply-To: <6234c0c60712250055g62b126c4t881dd77e8ee64334@mail.gmail.com>
Message-ID: <93043.37866.qm@web60321.mail.yahoo.com>

Dear Guoying,

Merry Christmas, thanks!

Electron phonon coupling constant \lambda is a
dimensionless parameter by its definition. 
At low temperatures (T) experimental electronic
specific heat C_{el}(T) is defined as 
C_{el}(T) = const N(0) (1 + \lambda) T, where N(0) is
taken from electronic structure calculations (i.e.
N(0) is the DOS at the Fermi level). Thus, \lambda can
be considered as a measure of the enhancement of the
electronic heat due to electron - phonon interacton.  


> However, a question confused me for a long  time, 
> that is, there is  no unit for the electron pnonon 
> coupling parameter  lambda.

I suggest, the best way is reading a textbook or
related papers to be not confused.

Please do not forget provide your affiliation.

Bests,
Eyvaz.

--- Guoying Gao <gaoguoying at gmail.com> wrote:

> Dear pwscf users,
> 
>          I have done electron-phonon coupling
> calculations for a
> period. However, a question confused me for a long
> time, that is,
> there is
> no unit for the electron pnonon coupling parameter
> lambda. Does anyone
> know the reason for this? Any help will be
> appreciated.
> 
> Merry Christmas!
> 
> Guoying
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


      ____________________________________________________________________________________
Never miss a thing.  Make Yahoo your home page. 
http://www.yahoo.com/r/hs

From akohlmey at cmm.chem.upenn.edu  Tue Dec 25 14:10:24 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 25 Dec 2007 08:10:24 -0500
Subject: [Pw_forum] About relaxation and cpmd
In-Reply-To: <13859583.505811198573757266.JavaMail.coremail@bj126app103.126.com>
References: <13859583.505811198573757266.JavaMail.coremail@bj126app103.126.com>
Message-ID: <7b6913e90712250510u8a254bei40b7e44375782c9d@mail.gmail.com>

On Dec 25, 2007 4:09 AM, oulihui666 <oulihui666 at 126.com> wrote:
> Dear all,
>     I have a naive problem, and need your help. I have not understanded this
> problem

you don't need "our" help, you need to read a textbook.

> for a long time, etc. the difference between relaxation and molecular
> dynamics(cpmd), I
> think that there is many steps in the process of relaxation, and every step
> denotes
> a intermediate, however, It also contains many intermediate in molecular
> dynamics
> simulation, I do not understand the difference between relxation and
> molecular
> dynamics(cpmd) at all times. Anyone who would give suggestion will be
> appreciated.

a very, very superficial explanation would be, that relaxation/geometry
optimization is like an MD at 0K (which it isn't).

please go to http://www.quantum-espresso.org and have a look at
the lecture slides available from there and then pick up a proper text
book and make sure you understand all the details.

best regards,
     axel.



>     Thanks in advance
>     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
> ======================================
> _______________________________________________
> 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 oulihui666 at 126.com  Tue Dec 25 14:15:43 2007
From: oulihui666 at 126.com (oulihui666)
Date: Tue, 25 Dec 2007 21:15:43 +0800 (CST)
Subject: [Pw_forum] k_max and k_min
Message-ID: <19213602.655641198588543353.JavaMail.coremail@bj126app103.126.com>

Dear all, 
  I want to ask a problem, when calculating NEB, we will set k_max and k_min, is there any principles about the settings of k_max and k_min in different systems? I need your help.
  Many thanks
  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 gaoguoying at gmail.com  Tue Dec 25 14:16:50 2007
From: gaoguoying at gmail.com (Guoying Gao)
Date: Tue, 25 Dec 2007 21:16:50 +0800
Subject: [Pw_forum] the unit of lambda
In-Reply-To: <93043.37866.qm@web60321.mail.yahoo.com>
References: <6234c0c60712250055g62b126c4t881dd77e8ee64334@mail.gmail.com>
	<93043.37866.qm@web60321.mail.yahoo.com>
Message-ID: <6234c0c60712250516t5512e39dgb707317aaefe93dc@mail.gmail.com>

Hi Eyvaz,
     Thanks for your kindly help.
     I have read some related papers. But I didn't find the reason.
Could you recommend me some papers?
Thanks again.
Guoying

National lab of superhard materials
Jilin University
P.R. of China

On Dec 25, 2007 6:53 PM, Eyvaz Isaev <eyvaz_isaev at yahoo.com> wrote:
> Dear Guoying,
>
> Merry Christmas, thanks!
>
> Electron phonon coupling constant \lambda is a
> dimensionless parameter by its definition.
> At low temperatures (T) experimental electronic
> specific heat C_{el}(T) is defined as
> C_{el}(T) = const N(0) (1 + \lambda) T, where N(0) is
> taken from electronic structure calculations (i.e.
> N(0) is the DOS at the Fermi level). Thus, \lambda can
> be considered as a measure of the enhancement of the
> electronic heat due to electron - phonon interacton.
>
>
> > However, a question confused me for a long  time,
> > that is, there is  no unit for the electron pnonon
> > coupling parameter  lambda.
>
> I suggest, the best way is reading a textbook or
> related papers to be not confused.
>
> Please do not forget provide your affiliation.
>
> Bests,
> Eyvaz.
>
>
> --- Guoying Gao <gaoguoying at gmail.com> wrote:
>
> > Dear pwscf users,
> >
> >          I have done electron-phonon coupling
> > calculations for a
> > period. However, a question confused me for a long
> > time, that is,
> > there is
> > no unit for the electron pnonon coupling parameter
> > lambda. Does anyone
> > know the reason for this? Any help will be
> > appreciated.
> >
> > Merry Christmas!
> >
> > Guoying
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
> -------------------------------------------------------------------
> Prof. Eyvaz Isaev,
> Theoretical Physics Department, Moscow State Institute of Steel & Alloys, Russia, and
> Condensed Matter Theory Group, Uppsala University, Sweden
> Eyvaz.Isaev at fysik.uu.se, eyvaz_isaev at yahoo.com
>
>
>       ____________________________________________________________________________________
> Never miss a thing.  Make Yahoo your home page.
> http://www.yahoo.com/r/hs
> _______________________________________________
> 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 Dec 25 15:59:07 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Tue, 25 Dec 2007 15:59:07 +0100
Subject: [Pw_forum] k_max and k_min
In-Reply-To: <19213602.655641198588543353.JavaMail.coremail@bj126app103.126.com>
References: <19213602.655641198588543353.JavaMail.coremail@bj126app103.126.com>
Message-ID: <7b6913e90712250659l277a5dfbg190255776d72f43b@mail.gmail.com>

dear lihui ou,

please consider handling one problem at a time
and not everything at the same time. based on your
recent questions, i strongly advise to first work on
your understanding of the elementary principles
of the kind of calculations you want to do.

this will then help you to understand a _lot_ of the
problems you have currently without having to ask
somebody as well as being able to comprehend
responses to your more advanced questions.

although it seems (to many) a very convenient
solution to fire a lot of questions to a user forum
or a mailing list and it may even work for a while,
but you also have to consider that you'll be wearing
out people quickly and on top of that make them even
less responsive to other people with equally legitimate
questions.

to cut a long story short. please be considerate in
what you ask and show people that you are willing
to do your part in understanding what you are doing.
this will be a help to everybody including yourself.

thanks and best regards,
    axel.

On 12/25/07, oulihui666 <oulihui666 at 126.com> wrote:
> Dear all,
>   I want to ask a problem, when calculating NEB, we will set k_max and
> k_min, is there any principles about the settings of k_max and k_min in
> different systems? I need your help.
>   Many thanks
>   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
> ======================================
> _______________________________________________
> 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 kddst2005 at yahoo.com.cn  Tue Dec 25 17:07:51 2007
From: kddst2005 at yahoo.com.cn (Dongdong Kang)
Date: Wed, 26 Dec 2007 00:07:51 +0800 (CST)
Subject: [Pw_forum] about 'md'
Message-ID: <636263.79858.qm@web92015.mail.cnb.yahoo.com>

Dear all
   
  I want to use 'md' (in pwscf) to calculate vibrational property about some materials. but when i check the output file, there aren't ion velocities in it.   How can i get ion velocities in 'md' ? 
  
thanks



Dongdong Kang 
National University of Defense Technology, P R China
410073, Hunan, Changsha

       
---------------------------------
??????????????????? 
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From manoj.warrier at gmail.com  Wed Dec 26 02:35:52 2007
From: manoj.warrier at gmail.com (Manoj Warrier)
Date: Wed, 26 Dec 2007 07:05:52 +0530
Subject: [Pw_forum] About relaxation and cpmd
In-Reply-To: <13859583.505811198573757266.JavaMail.coremail@bj126app103.126.com>
References: <13859583.505811198573757266.JavaMail.coremail@bj126app103.126.com>
Message-ID: <570912040712251735n3553c249v890d6391c7f8586d@mail.gmail.com>

Well .. you can do a MD to relax, but you cannot do a "relax" to
simulate dynamics :-).

Seriously speaking .. relaxing a group of atoms will be to get the
configuration of the atoms that have the lowest total energy. This can
be done by various simulation methods like: (i) Method of conjugate
gradients, (ii) Simulated Annealing, (iii) Genetic Algorithms, (iv) ??
Notes for these are available online at
http://beam.acclab.helsinki.fi/~knordlun/mc/ and a google (scholar)
search will lead to applications with examples.

In MD, relaxing a group of atoms involves using a NPT ensemble to get
the system to oscillate around zero pressure at temperature T by
changing the volume of the system. Simulated annealing or Genetic
Algorithm can usually take your atoms to a more global relaxed state
than your MD will.

Wondering what the experts' take will be on the above ...

Best Regards,
Manoj Warrier
Institute for Plasma Research,
BHAT, Gandhinagar, Gujarat,
India - 382428

On 25/12/2007, oulihui666 <oulihui666 at 126.com> wrote:
> Dear all,
>     I have a naive problem, and need your help. I have not understanded this
> problem
> for a long time, etc. the difference between relaxation and molecular
> dynamics(cpmd), I
> think that there is many steps in the process of relaxation, and every step
> denotes
> a intermediate, however, It also contains many intermediate in molecular
> dynamics
> simulation, I do not understand the difference between relxation and
> molecular
> dynamics(cpmd) at all times. Anyone who would give suggestion will be
> appreciated.
>     Thanks in advance
>     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
> ======================================
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>


-- 
Manoj Warrier
-------------------------------------------------
And everything should be possible with the
click of a mouse in my perfect world!!
-Lord Farquad
-------------------------------------------------
http://www.ipr.res.in/~manoj

From jibiaoli at gmail.com  Wed Dec 26 03:31:35 2007
From: jibiaoli at gmail.com (Clark Lee)
Date: Wed, 26 Dec 2007 10:31:35 +0800
Subject: [Pw_forum] About vibriational spectra
Message-ID: <b8b82da20712251831p2d7ef028sa9940a49f04e974f@mail.gmail.com>

Dear all,
How can i obtain a vibriational spectra (e.g. water on Pd) from ab initio
molecular dynamics simulations on the basis of the velocity-velocity
correlation functions. Thank you!
-- 
Yours sincerely,

Clark Lee

State Key Lab of Corrosion and Protection (SKLCP)
Institute of Metal Research (IMR)
Chinese Academy of Sciences (CAS), China
Phone: 024-23925323
Email: jibiaoli at gmail.com
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From limkr at umich.edu  Wed Dec 26 15:08:59 2007
From: limkr at umich.edu (Dong-Hee Lim)
Date: Wed, 26 Dec 2007 09:08:59 -0500
Subject: [Pw_forum] Error message from NEB calculation
Message-ID: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>

Dear All

I was wondering why the following error message occurs whenever I 
restart NEB calculations. For example, if I run a NEB calculation for 
48 hours, it runs without any trouble; however, if I run the NEB 
calculation for several hours and then try to restart it, it causes the 
following error.

I would appreciate if you let me know what the following error means...


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     from cdiaghg : error #      1204
     info =/= 0
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Sincerely,
Dong-Hee Lim

-- 
Dong-Hee Lim, Ph.D. candidate
Dept. of Civil and Environmental Engineering
University of Michigan


From eyvaz_isaev at yahoo.com  Wed Dec 26 16:50:33 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 26 Dec 2007 07:50:33 -0800 (PST)
Subject: [Pw_forum] Error message from NEB calculation
In-Reply-To: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>
Message-ID: <56870.55225.qm@web60319.mail.yahoo.com>

Dear Lim,

Please be not too lazy reading QE UserGide in /Doc. 
Below is a sketch from this manual:

Possible reasons for such behavior are not always
clear, but they typically fall into one of the
following cases:
   ??? serious error in data, such as bad atomic
positions or bad crystal structure/supercell;
   ??? a bad PP, typicall with a ghost, but also a
US-PP with non-positive charge density, leading to a
violation of positiveness of the S matrix appearing in
the US-PP formalism;
   ??? a failure of the algorithm performing subspace
diagonalization. The LAPACK algorithms used by
cdiaghg/rdiaghg are very robust and extensively
tested. Still, it may seldom happen that such
algorithms fail.
Try to use conjugate-gradient diagonalization
(diagonalization=???cg???), a slower but very robust
algorithm, and see what happens.

Bests,
Eyvaz.

--- Dong-Hee Lim <limkr at umich.edu> wrote:

> Dear All
> 
> I was wondering why the following error message
> occurs whenever I 
> restart NEB calculations. For example, if I run a
> NEB calculation for 
> 48 hours, it runs without any trouble; however, if I
> run the NEB 
> calculation for several hours and then try to
> restart it, it causes the 
> following error.
> 
> I would appreciate if you let me know what the
> following error means...
> 
> 
>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from cdiaghg : error #      1204
>      info =/= 0
>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> Sincerely,
> Dong-Hee Lim
> 
> -- 
> Dong-Hee Lim, Ph.D. candidate
> Dept. of Civil and Environmental Engineering
> University of Michigan
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


      ____________________________________________________________________________________
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From eyvaz_isaev at yahoo.com  Wed Dec 26 16:59:14 2007
From: eyvaz_isaev at yahoo.com (Eyvaz Isaev)
Date: Wed, 26 Dec 2007 07:59:14 -0800 (PST)
Subject: [Pw_forum] Error message from NEB calculation
In-Reply-To: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>
Message-ID: <487962.40645.qm@web60316.mail.yahoo.com>

Sorry, one more comment from the UserGuide, but I
think you should consider very seriously first  three
comments sent before:

- buggy libraries. Machine-optimized mathematical
libraries are very fast but sometimes not so robust
from a numerical point of view. Suspicious behavior:
you get an error that is not reproducible on other
 architectures or that disappears if the calculation
is repeated with even minimal changes in parameters.
One known case: HP-Compaq alphas with cxml libraries.
Try to use compiled BLAS and LAPACK (or better, ATLAS)
instead of machine-optimized libraries.

Bests,
Eyvaz.

--- Dong-Hee Lim <limkr at umich.edu> wrote:

> Dear All
> 
> I was wondering why the following error message
> occurs whenever I 
> restart NEB calculations. For example, if I run a
> NEB calculation for 
> 48 hours, it runs without any trouble; however, if I
> run the NEB 
> calculation for several hours and then try to
> restart it, it causes the 
> following error.
> 
> I would appreciate if you let me know what the
> following error means...
> 
> 
>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
>      from cdiaghg : error #      1204
>      info =/= 0
>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
> 
> Sincerely,
> Dong-Hee Lim
> 
> -- 
> Dong-Hee Lim, Ph.D. candidate
> Dept. of Civil and Environmental Engineering
> University of Michigan
> 
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


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


      ____________________________________________________________________________________
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know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 


From giannozz at nest.sns.it  Wed Dec 26 18:27:44 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 26 Dec 2007 18:27:44 +0100
Subject: [Pw_forum] About nelec and tot_charge again
In-Reply-To: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>
References: <12514118.1058181198494707550.JavaMail.coremail@bj126app104.126.com>
Message-ID: <200712261827.44933.giannozz@nest.sns.it>

On Monday 24 December 2007 12:11, oulihui666 wrote:

> I intend to ask wheather I could add a extra electron and +1 charge
> simultaneously?

you can add an extra electron by setting variable "nelec" to the desired
charges. The code will automatically add a neutralizing background (it
must! the energy of a charged supercell is infinite). In practice, the energy
is calculated as usual, but the divergent terms will be calculated as if 
the system was neutral. For a molecule the energy so obtained will 
converge for increasing size of the supercell to the true energy of the
charged molecule; there are various tricks to speedup the convergence
(e.g. the Makov-Payne correction). Formation energies of charged defects
can also be calculated but it is a more tricky business.

By the way, all this has been explained 2n+1 times.

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From giannozz at nest.sns.it  Wed Dec 26 18:28:29 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 26 Dec 2007 18:28:29 +0100
Subject: [Pw_forum] optimizing pw input parameters
In-Reply-To: <286763.84392.qm@web30605.mail.mud.yahoo.com>
References: <286763.84392.qm@web30605.mail.mud.yahoo.com>
Message-ID: <200712261828.29666.giannozz@nest.sns.it>

On Sunday 23 December 2007 09:23, meisam aghtar wrote:

> I have to mention that there is overlap in davidson diagonalization.

of course there is. The davidson algorithm generates a subspace of 
trial and correction vectors and performs a generalized diagonalization 
in the subspace: h v_i = e_i s v_i, where s is the "overlap matrix" 
between trial+correction vectors. In the past there used to be another
version of the algorithm that used a "normal" diagonalization instead: 
h v_i = e_i v_i . This is the reason for the message.

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From giannozz at nest.sns.it  Wed Dec 26 18:37:05 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Wed, 26 Dec 2007 18:37:05 +0100
Subject: [Pw_forum] Error message from NEB calculation
In-Reply-To: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>
References: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>
Message-ID: <200712261837.05062.giannozz@nest.sns.it>

On Wednesday 26 December 2007 15:08, Dong-Hee Lim wrote:

> I would appreciate if you let me know what the following error means...
>[...] from cdiaghg : error #      1204
>      info =/= 0

I would appreciate if people stop asking again and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
and again and again and again and again and and again and again
the same question. Please look for 'cdiaghg' in the documentation
and in the archives of the mailing list
-- -
Paolo Giannozzi, Democritos and Udine University 

From akohlmey at cmm.chem.upenn.edu  Wed Dec 26 21:04:29 2007
From: akohlmey at cmm.chem.upenn.edu (Axel Kohlmeyer)
Date: Wed, 26 Dec 2007 21:04:29 +0100
Subject: [Pw_forum] Error message from NEB calculation
In-Reply-To: <200712261837.05062.giannozz@nest.sns.it>
References: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>
	<200712261837.05062.giannozz@nest.sns.it>
Message-ID: <7b6913e90712261204w4d098947gffa3656915e0fe0a@mail.gmail.com>

hi paolo,

how about changing the error message that spells out in detail
what to do and also generate a URL that directly points to the
troubleshooting part of the documentation on quantum-espresso.org
and/or to start a web search, e.g., on google with querying for
"cdiaghg error site:pwscf.org"?

i'm "in transit" at the moment, but give me a couple of days and
i could generate a patch of that kind, so that perhaps 50% of the
people will try looking at the archives or the docs before asking here.
the fact that the error message looks a bit cryptic (also to me initially),
may be the reason that people tend to have this knee-jerk reaction
to directly post to the mailing list (for some i assume even dispite
knowing better or being told so before...).

other than that i can only encourage people that have had this kind
of problem before and got told the same stuff to respond first and thus
keep you from having to go over the same question again and again
and .... ;-)

this forum has improved a lot over the last years (in terms of topics
and the number of people answering) and is (to me at least) becoming
increasingly interesting to follow, and it would be a big help if
people with less experience, could handle the "simple" questions.

ciao,
   axel.


On 12/26/07, Paolo Giannozzi <giannozz at nest.sns.it> wrote:
> On Wednesday 26 December 2007 15:08, Dong-Hee Lim wrote:
>
> > I would appreciate if you let me know what the following error means...
> >[...] from cdiaghg : error #      1204
> >      info =/= 0
>
> I would appreciate if people stop asking again and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> and again and again and again and again and and again and again
> the same question. Please look for 'cdiaghg' in the documentation
> and in the archives of the mailing list
> -- -
> Paolo Giannozzi, Democritos and Udine University
> _______________________________________________
> 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  Thu Dec 27 07:21:42 2007
From: kazempoor2000 at yahoo.com (ali kazempoor)
Date: Wed, 26 Dec 2007 22:21:42 -0800 (PST)
Subject: [Pw_forum] spilling parameter
Message-ID: <402163.31910.qm@web33104.mail.mud.yahoo.com>

Dear all
 Irun scf for a  MnAs nanowire and after projwfc the
spilling parameter is very high(0.98).
which parameter  should i change?
thanks


      ____________________________________________________________________________________
Be a better friend, newshound, and 
know-it-all with Yahoo! Mobile.  Try it now.  http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ 


From giannozz at nest.sns.it  Thu Dec 27 11:39:16 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 27 Dec 2007 11:39:16 +0100
Subject: [Pw_forum] about 'md'
In-Reply-To: <636263.79858.qm@web92015.mail.cnb.yahoo.com>
References: <636263.79858.qm@web92015.mail.cnb.yahoo.com>
Message-ID: <200712271139.16430.giannozz@nest.sns.it>

On Tuesday 25 December 2007 17:07, Dongdong Kang wrote:

>   I want to use 'md' (in pwscf) to calculate vibrational property about
> some materials. but when i check the output file, there aren't ion
> velocities in it.   How can i get ion velocities in 'md' ?

you have to modify PW/dynamics-module.f90 so that saves somewhere 
the velocities (they should be in array "vel"). PWscf uses the plain verlet
algorithm, not the velocity verlet. Until  now nobody has felt the need to
know about velocities, so they were not saved

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From giannozz at nest.sns.it  Thu Dec 27 11:40:20 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 27 Dec 2007 11:40:20 +0100
Subject: [Pw_forum] Machine-specific FFT's
Message-ID: <200712271140.20959.giannozz@nest.sns.it>

Can anybody confirm usage (or non-usage due to problems)
of the following machine-specific FFT's ? in absence of 
feedback, they will be removed from the next version:
- Dec/Compaq/HP DXML/CXML (-DDXML)
- SGI compib (-D__COMPLIB)
- Intel MKL v.8 (-D__FFTMKL8)
I would also appreciate hearing from people using
v.3 of FFTW (-D__FFTW3), if any

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From marzari at MIT.EDU  Thu Dec 27 12:48:13 2007
From: marzari at MIT.EDU (Nicola Marzari)
Date: Thu, 27 Dec 2007 06:48:13 -0500
Subject: [Pw_forum] about 'md'
In-Reply-To: <200712271139.16430.giannozz@nest.sns.it>
References: <636263.79858.qm@web92015.mail.cnb.yahoo.com>
	<200712271139.16430.giannozz@nest.sns.it>
Message-ID: <477390FD.9050500@mit.edu>



As a side note, if you have the positions along a trajectories,
you can reverse engineer the velocities:

v(t)=(x(t+delta)-x(t-delta))/(2*delta)

(easy to see: do a series expansion of x(t), around t, in powers of
the timestep delta).

			nicola


Paolo Giannozzi wrote:
> On Tuesday 25 December 2007 17:07, Dongdong Kang wrote:
> 
>>   I want to use 'md' (in pwscf) to calculate vibrational property about
>> some materials. but when i check the output file, there aren't ion
>> velocities in it.   How can i get ion velocities in 'md' ?
> 
> you have to modify PW/dynamics-module.f90 so that saves somewhere 
> the velocities (they should be in array "vel"). PWscf uses the plain verlet
> algorithm, not the velocity verlet. Until  now nobody has felt the need to
> know about velocities, so they were not saved
> 
> Paolo


-- 
---------------------------------------------------------------------
Prof Nicola Marzari   Department of Materials Science and Engineering
13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

From kondor.jess at gmail.com  Thu Dec 27 18:59:45 2007
From: kondor.jess at gmail.com (Jess Kondor)
Date: Thu, 27 Dec 2007 11:59:45 -0600
Subject: [Pw_forum] cvs version in parallel, a problem
Message-ID: <1d9d5d9d0712270959i6ae1c7e9j4729d9564f19c799@mail.gmail.com>

Dear developers,

 I understand, that CVS version is under development and might not work, but
in that version a bug in Berry Phase calculation is fixed, so I prefer to
use CVS version instead official one.

I have noticed that pwscf  crashes in parallel (compiled by ifort 9.1,
mvapich) , when more than 2 cores is used. Test example is an 'atom.in' file
provided in ' tests/' . The error message is:
.....
     Initial potential from superposition of free atoms

     starting charge    6.00000, renormalised to    6.00000

     negative rho (up, down):  0.101E-04 0.000E+00
     Starting wfc are    4 atomic +    2 random wfc
mpirun_rsh: Abort signaled from [1]

Checking atom...1 - MPI_REQUEST_FREE : Invalid mpi_request handle
[1] [] Aborting Program!
done.

Does anybody notice the same problems?

 Best wishes,

-- 
=====================================
Jess Kondor,
PhD Student

PICYT, Av. Venustiano Carranza 2425-A,
San Luis Potos? 78210, M?xico
=====================================
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From giannozz at nest.sns.it  Thu Dec 27 19:03:28 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 27 Dec 2007 19:03:28 +0100
Subject: [Pw_forum] Error message from NEB calculation
In-Reply-To: <7b6913e90712261204w4d098947gffa3656915e0fe0a@mail.gmail.com>
References: <20071226090859.985f68i0lc800k4k@web.mail.umich.edu>
	<200712261837.05062.giannozz@nest.sns.it>
	<7b6913e90712261204w4d098947gffa3656915e0fe0a@mail.gmail.com>
Message-ID: <200712271903.28692.giannozz@nest.sns.it>

On Wednesday 26 December 2007 21:04, Axel Kohlmeyer wrote:

> how about changing the error message that spells out in detail
> what to do and also generate a URL that directly points to the
> troubleshooting part of the documentation on quantum-espresso.org
> and/or to start a web search, e.g., on google with querying for
> "cdiaghg error site:pwscf.org"?

in order to spell out "in detail" what the error message mean, one
has to know in detail why the error occurs. Years ago I spent several 
days chasing this error. Finally I gave up: it was a random error, 
occurring in a library, even on one of the best machines available 
at the time (sp3); guess what may happen on a PC (Piece of Crap). 
Unless somebody proves the opposite, I safely assume that it is 
not a bug in the code. This completes my assignement :-)

I am also very dissatisfied with the status of error reporting in 
q-e, for multiple reasons, but any improvement would require 
a new interface to the error handling routine; since there are 
2354 calls in the q-e suite as of today (counted using:
"grep errore */*f90| grep -i call | wc -l") my guess is that this 
is not going to happen anytime soon. Suggestions welcome.

> i'm "in transit" at the moment, but give me a couple of days and
> i could generate a patch of that kind

Solutions are much more welcome than suggestions!

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From giannozz at nest.sns.it  Thu Dec 27 19:04:37 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Thu, 27 Dec 2007 19:04:37 +0100
Subject: [Pw_forum] About vibriational spectra
In-Reply-To: <b8b82da20712251831p2d7ef028sa9940a49f04e974f@mail.gmail.com>
References: <b8b82da20712251831p2d7ef028sa9940a49f04e974f@mail.gmail.com>
Message-ID: <200712271904.37347.giannozz@nest.sns.it>

On Wednesday 26 December 2007 03:31, Clark Lee wrote:

> How can i obtain a vibrational spectra (e.g. water on Pd) from ab initio
> molecular dynamics simulations on the basis of the velocity-velocity
> correlation functions.


do you want to know about the method or about a code doing this?
for the former, look for a paper by Jorge Kohanoff, 1992 I think.
For the latter: there is no tool in Q-E performing this task; you 
have to write a small piece of code

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University 

From mousumi at jncasr.ac.in  Fri Dec 28 06:34:42 2007
From: mousumi at jncasr.ac.in (Mousumi Upadhyay Kahaly)
Date: Fri, 28 Dec 2007 11:04:42 +0530 (IST)
Subject: [Pw_forum] To get layer projected DOS
Message-ID: <34504.202.54.54.226.1198820082.squirrel@202.54.54.226>

Dear All,

I wish to plot electronic DOS of each layer in a layered system.
How to get layer-by-layer DOS from PWSCF postprocessing? Any inputs
in this regard will help a lot. Thanking you in anticipation,

Mousumi Upadhyay Kahaly
Theoretical Sciences Unit,
JNCASR, Bangalore, India.

From r95222066 at ntu.edu.tw  Fri Dec 28 10:57:59 2007
From: r95222066 at ntu.edu.tw (r95222066 at ntu.edu.tw)
Date: Fri, 28 Dec 2007 17:57:59 +0800
Subject: [Pw_forum] =?big5?b?QaFAcXVlc3Rpb24gYWJvdXQgTERBK1UgY2FsY3VsYXRp?=
	=?big5?b?b24gYW9idXQgVmFuYWRpdW0JPw==?=
Message-ID: <20071228175759.6uu076wvfogg0kos@wmail1.cc.ntu.edu.tw>

Dear all,
       I would like to ask a question about the question i encounter  
.I calculated the transition metal element Vanadium "V" about LDA+U  
calculation ,the scf output file show
--------------------------------------------------------------------
from tabd : error #         1
      pseudopotential not yet inserted
--------------------------------------------------------------------
I check the pwscf forum ,it suggest me to correct the  tabd.f90 file  
in PW.x code , so I would like to ask what is the "occ_loc" number for  
Vanadium "V" ?

Thanks a lot
              Bing-hong Chen
                        Physics department,National Taiwan Unverisity,Taiwan

From hqzhou at nju.edu.cn  Fri Dec 28 11:58:06 2007
From: hqzhou at nju.edu.cn (Huiqun Zhou)
Date: Fri, 28 Dec 2007 18:58:06 +0800
Subject: [Pw_forum]
	=?iso-8859-1?q?A=A1=40question_about_LDA+U_calculation?=
	=?iso-8859-1?q?_aobut_Vanadium=09=3F?=
References: <20071228175759.6uu076wvfogg0kos@wmail1.cc.ntu.edu.tw>
Message-ID: <004801c84940$86949c40$1d00a8c0@solarflare>

Didn't you find an explanation for occ_loc in the source code? It's "the 
total
number of d electrons", so occ_loc for V should be 3.0.

Cheers,

Dr. Huiqun Zhou
@Earth Sciences, Nanjing University, China


----- Original Message ----- 
From: <r95222066 at ntu.edu.tw>
To: <pw_forum at pwscf.org>
Sent: Friday, December 28, 2007 5:57 PM
Subject: [Pw_forum] A?@question about LDA+U calculation aobut Vanadium ?


> Dear all,
>       I would like to ask a question about the question i encounter
> .I calculated the transition metal element Vanadium "V" about LDA+U
> calculation ,the scf output file show
> --------------------------------------------------------------------
> from tabd : error #         1
>      pseudopotential not yet inserted
> --------------------------------------------------------------------
> I check the pwscf forum ,it suggest me to correct the  tabd.f90 file
> in PW.x code , so I would like to ask what is the "occ_loc" number for
> Vanadium "V" ?
>
> Thanks a lot
>              Bing-hong Chen
>                        Physics department,National Taiwan 
> Unverisity,Taiwan
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
> 


From giannozz at nest.sns.it  Fri Dec 28 21:16:29 2007
From: giannozz at nest.sns.it (Paolo Giannozzi)
Date: Fri, 28 Dec 2007 21:16:29 +0100
Subject: [Pw_forum] cvs version in parallel, a problem
In-Reply-To: <1d9d5d9d0712270959i6ae1c7e9j4729d9564f19c799@mail.gmail.com>
References: <1d9d5d9d0712270959i6ae1c7e9j4729d9564f19c799@mail.gmail.com>
Message-ID: <200712282116.29586.giannozz@nest.sns.it>

On Thursday 27 December 2007 18:59, Jess Kondor wrote:

>  I understand, that CVS version is under development and might not work,
> but in that version a bug in Berry Phase calculation is fixed, so I prefer
> to use CVS version instead official one.
>
> I have noticed that pwscf  crashes in parallel (compiled by ifort 9.1,
> mvapich) , when more than 2 cores is used. 

since you are barve enough to use CVS, you should also learn 
how to use "cvs update -D 'date'" or "cvs update -r 'revision'" 
to find when and why a problem started! There is some work 
going on in parallelism (task group impllementation in PW) right 
now. You can follow it on the web-cvs interface. The last changes 
were made this afternoon (Central Europe Time). If your problem 
is not fixed in the next few days, and if you have evidence that it 
is due to a bug in the code and not to a bug in anything else, please 
submit your problem again

Paolo
-- 
Paolo Giannozzi, Democritos and Udine University