[Pw_forum] FW: cell optimization results seems to be a little strange

[vega lew]

Dear all,

Thank to all your help, I could run a Q-E calculation on my cluster more 
correctly. Now I can learn to do some 
simple calculations.

My first job is to calculate the Anatase-TiO2 lattice cell parameter using Q-E 
and compare it with literature.
I have tested the BFGS for vc-relax, but the cell parameters changed so much 
that an error was occured with
the information 'non orthogonal operation'. Then I used a symmetry-conserving 
algorithm as the QE manual
said. The input file as following,
 

   title = 'Anatase lattice' ,
 calculation = 'vc-relax' ,
restart_mode = 'from_scratch' ,
  outdir = '/home/vega/espresso-4.0/tmp/' ,
  wfcdir = '/tmp/' ,
  pseudo_dir = '/home/vega/espresso-4.0/pseudo/' ,
  prefix = 'Anatase lattice default' ,
 disk_io = 'none' ,
   etot_conv_thr = 0.00735 ,
   forc_conv_thr = 0.0011668141375 ,
   nstep = 1000 ,
 /
 
   ibrav = 6,
   celldm(1) = 7.135605333,
   celldm(3) = 2.5121822033898305084745762711864,
 nat = 12,
ntyp = 2,
 ecutwfc = 25 ,
 ecutrho = 200 ,
 /
 
conv_thr = 7.3D-8 ,
 /
 
ion_dynamics = 'damp' ,
 /
 
   cell_dynamics = 'damp-w' ,
 /
ATOMIC_SPECIES
   Ti   47.86700  Ti.pw91-sp-van_ak.UPF 
O   15.99940  O.pw91-van_ak.UPF 
ATOMIC_POSITIONS angstrom 
   Ti  0.00.00.0
   Ti  1.888001.888004.74300
   Ti  0.01.888002.37200
   Ti  1.888000.07.11500
O  0.00.01.97300
O  1.888001.888006.71600
O  0.01.888004.34500
O  1.888000.09.08800
O  1.888000.05.14100
O  0.01.888000.39800
O  1.888001.888002.77000
O  0.00.07.51300
K_POINTS automatic
 7 7 3   1 1 1 

The calculation can be done nearly 600 fs. The last few lines of results file 
is shown at the bottom.
But the cell parameters for Anatase lattice seems to be not perfectly match the 
results in literature.
In the literature, Journal of Physical Chemistry B, 2006, 110, 7464, the author 
used  a conjugate-gradient 
or quasi-Newton scheme as implemented in VASP to optimaize the geometries. And 
the cell parameters
are a = b = 3.803 A c = 9.603 A c/a = 2.525. But my Q-E result, a= 3.7546166A 
b= 3.75461729A c= 9.3911A
seems to be much smaller than his. I tried times times again, even, the 
starting geometry is from the 
exprimental data for Journal of  the American Society, 1987,109, 3639, which 
was also cited by him, the
result was still that small. 

I also have tested it in CASTEP, using BFGS and same precision. The CASTEP 
results were a = b =3.798668A
c = 9.693431A c/a = 2.5518, which seemed to be more close to the literature 
results. The starting geometry
was also from Journal of  the American Society, 1987,109, 3639. 

I think maybe some parameter in my Q-E input file was wrong. Could you please 
point it to me?

thank you for reading. I am waiting for your responding.

Vega Lew
PH.D Candidate in Chemical Engineering
State Key Laboratory of Materials-oriented Chemical Engineering
College of Chemistry and Chemical Engineering
Nanjing University of Technology, 210009, Nanjing, Jiangsu, China


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[Pw_forum] New BFGS file updated and the results is coming up.

[Nicola Marzari]

> 
> I'm look forwar for your advice.


Try rutile. Try Ti metal. Try an oxygen molecule. Do they all work ?

nic


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13-5066   MIT   77 Massachusetts Avenue   Cambridge MA 02139-4307 USA
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[Pw_forum] FW: cell optimization results seems to be a little strange

[Holger Hesske]

 
  Dear vega,

  next to the suggestion of Lorenzo to use the bfgs algorithm, the point in 
your input is the missing timestep for the cell dynamics with the 
Wentzcovitch algorithm. (see quantum-wiki) It looks like you got a 
non-evolving (or almost non-evolving) dynamics.
A second, more general remark on you input: Set up only the variables you 
really need (as Axel pointet out in several mails before: every non-written 
line is per definition a correct one).
It doesn't make any sense to set numbers with more than 14 digits (the code 
does not handle this) and in most cases 8 digits is more than enough, 
Think about, why you set etot_conv_thr so tight (don't mix it up with 
conv_thr, which seemed to be sloppy for this calculation ), while you set 
forc_conv_thr to be really sloppy? (Btw, is there any reason to set the 
cutoffs/thresholds to such precision?)

Hope this helps,

Holger 


-- 
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Inst.f.Chemie-/Bioingenieurwissenschaft.
Wolfgang-Pauli-Str. 10
ETH H?nggerberg, HCI E 133
CH-8093 Z?rich
Tel: +41 44 633 66 19
Fax: +41 44 632 11 63
E-Mail: holger.hesske at chem.ethz.ch

[Pw_forum] FW: cell optimization results seems to be a little strange

[Lorenzo Paulatto]

On Gio, Luglio 3, 2008 16:00, vega lew wrote:
>  I have tested the BFGS for vc-relax, but the cell parameters changed so
>  much that an error was occured with the information 'non orthogonal
> operation'.

This error should be fixed in CVS version of QE, if you wish to use bfgs
you can wait for QE 4.0.1 (which should be out soon) or overwrite the file
PW/stress.f90  with the one I've attached (and recompile pw.x).

Hope this helps.

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



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[Pw_forum] Small U for Co in ZnO for LDA+U

[Nektarios Lathiotakis]

Hi all,

the option 'atomic' is the default and maybe that should change? I dont
know. It created
me a lot of trouble however. I confirm Shu-jun numbers (2.6 occupations)...
I get the same.
I think we used the same functional and consequently potentials for
Zn, O, Co (PBE functional).

Shu-jun, did you use the same pseudo for Co in ZnO and SnO2?

With the 'atomic' option  in this case , U_Co=0.5 is enough to push all
Co-d states into the valence. The rule I found is that the U_Co with option
'atomic' has the same effect as 8*U with option 'ortho-atomic' on the Co-d
projected DOS.

So the self consistent value of Shu-jun correspond to U=2.5eV with
ortho-atomic. Of course this applies to
the position of Co-d occupied bands. Dont know about other properties. I
will have to
repeat calculations with 'ortho-atomic' or 'norm-atomic' option.

Thanks for the discussion
Nektarios

On Thu, Jul 3, 2008 at 10:16 AM, Nicola Marzari  wrote:

>
>
>
> Dear Shu-jun, All,
>
>
> I get very nervous about using U with non-normalized occupations. Even
> if U can have some amount of pseudopotential dependency, using it
> with unnormalized projectors really messes up any meaningful discussion
> of occupation values and U values.
>
> And of course referees would go nuts at seeing that a U=0.3eV is
> relevant - the reason is that that number doesn't really make sense.
>
> To me, it's an option ("atomic") that should be removed altogether from
> the code - others might have other opinions, but if we leave it as it
> stands, we risk creating an enormous amount of headaches down the line.
>
>nicola
>
>
>
>
> ??? Shu-jun Hu wrote:
> > Dear All,
> >
> > I would post my comments on the topic of LDA+U calculation of small U_Co.
> >
> > (1) The self-consistently calculated U_Co is indeed sensitive to the
> oxidation
> > state of Co. In Co-doped ZnO DMS, the value is about 0.31 eV, a very
> "small"
> > number. However, in Co-doped SnO2, we got a "reasonable" value of 3.7 eV.
> > U_projection_type is specified as the default (atomic) in both cases
> during the
> > calculation of U_Co.
> >
> > (2) The calculated band structure is much sensitive to the value of U_Co
> and
> > U_Co=0.31 eV does have a significant effect with respect to U=0.
> U_Co=0.31 eV can
> > well fit the experimental results (APL 84 4233 (2004), and also J. Appl.
> Phys. 103
> > 07D130 (2008)), where the occupied Co:3d majority state are deep in the
> valence
> > band rather than in the gap. If U_Co=2 to 5 eV is implemented, Nektarios
> is right:
> > a Co-d projected DOS far deep into the valence (completely non sense).
> >
> > (3) The occupation is larger than 1 but not less than 1 in the "atomic"
> case. A
> > piece of output file is listed in the end.
> >
> > Best wishes.
>
>
>
>
> --
> -
> 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
>



-- 

Dr. Nektarios N. Lathiotakis

Theoretical and Physical Chemistry Institute
National Hellenic Research Foundation
Vass. Constantinou 48, GR-11635,
Athens, Greece

Tel: +30 210 7273805 FAX: +30 210 7273794
Inst. secretary: +30 210 7273792, +30 210 7273795
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[Pw_forum] the wave function after scf calculation

[Lorenzo Paulatto]

On Gio, Luglio 3, 2008 13:46, meisam aghtar wrote:
>  Dear all
>  ?how can i get the converged wave function?in a?scf calculation?

Dear Meisam,
you don't have one wavefunction, but one Kohn-Sham single-particle
wavefunction per kpoint per band. You can use pp.x to extract them after
the calculation is finished.

Please see the pp.x documentation for details (espresso/Doc/INPUT_PP for
Q.E 3.x, espresso/Doc/INPUT_PP.html for qe 4.0)

regards

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



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[Pw_forum] complex band of Cu (fwd)

[Manoj Srivastava]

Dear PWSCF users, 
my advisor is interested in the following question. Any suggestions?

-manoj 
-- Forwarded message --
Date: Thu, 03 Jul 2008 11:38:14 -0400
From: Xiaoguang Zhang 
Reply-To: zhangx at ornl.gov
To: Manoj Srivastava , pw_forum at pwscf.org
Cc: zhangx at ornl.gov
Subject: Re: [Pw_forum] complex band of Cu (fwd)

Thanks for the reply. Even though we're experimenting with the (100) 
direction which does allow a 2 atom/cell tetragonal unit which yields 
the correct band structure, we are really interested in the (111) 
complex bands. Why is it necessary to use a3 to define the transport 
direction? Wouldn't it be simpler and conceptually clearer to define the 
transport direction to be the norm of the base plane?
Thanks,
Xiaoguang

Manoj Srivastava wrote:
> 
> -- Forwarded message --
> Date: Wed, 2 Jul 2008 08:01:19 +0200
> From: Alexander 
> Reply-To: PWSCF Forum 
> To: pw_forum at pwscf.org
> Subject: Re: [Pw_forum] complex band of Cu
> 
> Dear Manoj 
> The PWCOND code works only for monoclinic cells
> where the a3 vector of the unit cell (defining the transport direction) is 
> ORTHOGONAL to both a1 and a2. You SHOULD therefore use the tetragonal unit 
> cell with two atoms per cell.
> Regards,
> Alexander
>  
> 
> On Tuesday 01 July 2008 21:31, Manoj Srivastava wrote:
> 
>>Dear PWSCF users,
>> I have been trying to calculate the band structure of bulk Cu. I tried
>>two different kind of unit cells, 2 atoms tetragonal and 1 atom
>>rhombohedron. In case of tetragonal cell, i get the right band structure,
>>but in the case of rhombohedron, d bands of Cu are not at the right place.
>>I believe that these calculations should not depend on the choice of unit
>>cell. I would appreiate if someone could tell me what am I doing wrong?
>>Attached is the band-structure file I get for rhombohedron unit cell and
>>my input file is as follows-
>>
>>
>>ibrav=0
>>celldm(1)=6.73
>>nat= 1,
>>ntyp= 1,
>>ecutwfc =50.0,
>>occupations= 'smearing',
>>smearing='gaussian',
>>degauss=0.01
>> /
>> 
>>conv_thr = 1.0e-8
>>mixing_beta=0.7
>> /
>> ATOMIC_SPECIES
>> Cu   63.55  Cu.pbe-paw_kj.UPF
>> ATOMIC_POSITIONS
>>  Cu 0.0 0.0 0.0
>>K_POINTS (automatic)
>>4 4 4 0 0 0
>>CELL_PARAMETERS
>>0.5 -0.5  0.0
>>0.5  0.5  0.0
>>0.5  0.0  0.5
>>
>># complex bands of cu along the 001 direction K_perp=0
>>cat > cu.cond.in << EOF
>> 
>>outdir='$TMP_DIR/'
>>prefixl='cu'
>>band_file ='bands.cu'
>>ikind=0
>>energy0=10.d0
>>denergy=-0.04d0
>>ewind=3.d0
>>epsproj=1.d-6
>> /
>>1
>>0.0 0.0 1.0
>>500
>>EOF
>>
>>Regards,
>>Manoj Srivastava
>>Graduate Student
>>University of Florida
>>Gainesville, USA.
>>
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[Pw_forum] FW: cell optimization results seems to be a little strange

[Axel Kohlmeyer]

On Fri, 4 Jul 2008, vega lew wrote:

VL> > Think about, why you set etot_conv_thr so tight (don't mix it up with 
VL> > conv_thr, which seemed to be sloppy for this calculation ), while you set 
VL> > forc_conv_thr to be really sloppy? (Btw, is there any reason to set the 
VL> > cutoffs/thresholds to such precision?)
VL> 
VL> Many litterature doing so. The force threshold is usually set as 0.03eV and 
0.05eV
VL> for larger system. the cutoff in literature can be 380 or 400eV sometimes.
VL> I'm only doing repeat work and learning how to do a perfect calculation.
VL> Also the conv_thr and etot_conv_thr is taken from CASTEP calculation 
directly. Others

please note that convergence parameters can be _very_ arbitrary
between different codes and they can be in very strange units.


VL> doing so of the same system is the only reason. I'm a beginner of 
VL> PWscf and DFT calculation. So I think doing repeat work of others 
VL> and discuss with skilled people may be the best way for me. What I'm 
VL> doing now is something more like a homework rather than the research 
VL> work. I'm learning to using PWscf. Thank you for your help.

before going any further with running big calculations. try
smaller ones. and have you checked the requirements for each 
pseudopotential? is your stress tensor converged wrt. wavefunction 
_and_ density cutoff? ...and k-points? you are using vanderbilt 
ultrasoft pseudopotentials and they can require unexpectedly high 
density cutoffs. if i remember correctly. you are also not mentioning 
whether the reference you are comparing to is using the _same_ 
functional that you are using. different functionals 
tend to over/underestimate lattice parameters differently.

cheers,
   axel.

VL> 
VL> 
VL> Vega Lew
VL> PH.D Candidate in Chemical Engineering
VL> 
VL> State Key Laboratory of Materials-oriented Chemical Engineering
VL> College of Chemistry and Chemical Engineering
VL> Nanjing University of Technology, 210009, Nanjing, Jiangsu, China
VL> 
VL> 
VL> 
VL> _
VL> Connect to the next generation of MSN Messenger?
VL> 
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-- 
===
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[Pw_forum] How to compute surface energy and adsorbed energy ?

[wangqj1]

 Dear pwscf users;
 Could someone tell me 'how to compute surface energy and adsorbed energy '?
 whether the surface energy is the whole energy or not ? 
 I am looking forward to your advice .
Thanks!
 
 
 
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[Pw_forum] "from pzpotrf : error # 1 problems computing cholesky decomposition"

[Lorenzo Paulatto]

On Mer, Luglio 2, 2008 13:06, vega lew wrote:
>  I have tested a scecond run the error occurred at the same point.
>  but the error message seems to be a little different. This time is
>  "  from  pzpotrf  : error #   841" not the "error #  1"

Thank you, unluckily the two errors are probably equivalent.

I'm not really in that part of code, anyway in order to find out any more
I should know if pw was using the distributed algorithm: just paste the
full output as it is printed in the first lines.

It may be that during a vc-relax step the cell shrunk a lot so that the
atoms got very close (you can check this). It happened to me a few times,
but it is rather uncommon. You can try changing the vc-relax parameters to
 take smaller steps.

Anyway I'm going to ask C. Cavazzoni, who implemented that algorithm, to
see if he can provide some insight.

bye

-- 
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[Pw_forum] How to compute surface energy and adsorbed energy ?

[Nicola Marzari]

wangqj1 wrote:
>  Dear pwscf users;
>  Could someone tell me 'how to compute surface energy and adsorbed energy '?
>  whether the surface energy is the whole energy or not ? 
>  I am looking forward to your advice .
> Thanks!
>  
>  


To follow-up on Stefano Baroni's suggestions, you could also look
at the first lectures of:

http://ocw.mit.edu/OcwWeb/Materials-Science-and-Engineering/3-320Spring-2005/CourseHome/index.htm

Both Lab 1 (classical potentials) and Lab 2 (quantum, using 
Quantum-ESPRESSO) deal with surface energies.

nicola


-
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tel 617.4522758 fax 2586534 marzari at mit.edu http://quasiamore.mit.edu

[Pw_forum] How to compute surface energy and adsorbed energy ?

[Stefano Baroni]

On Jul 3, 2008, at 4:45 AM, wangqj1 wrote:

>  Dear pwscf users;

Dear Mr. Unknown

>  Could someone tell me 'how to compute surface energy and adsorbed  
> energy '?

I am afraid, this question would be more appropriate for your  
supervisor than for this forum.

in any event, think of the definition of surface energy:
"surface energy" = energy necessary to cut an infinite solid into two  
semi-infinite parts (or in many slabs, for that matter, provided you  
count properly the number of slabs). right? now you can calculate the  
energy of bulk system (the result is infiite: what you get is an  
energy per unit volume, or an energy per atom). you can also calculate  
the energy of a system made of many (infinite, because of periodic  
boundary conditions) slabs. The enrgy per atom will be different. the  
difference will be proprortional to the surface area ... can you see  
now how the calculation would proceed?

The same would apply to "adsorption" (NOT "adsorbed") energy = energy  
of a surface (or a slam, for that matter) with an adsorbed molecule,  
minus the sum of energy of an isolated (clean) surface and of an  
isolated molecule.

>  whether the surface energy is the whole energy or not ?

do not undesrtand what you mean. think of the definitiion above

>  I am looking forward to your advice .
> Thanks!

would be so kind as to provide your name and full affiliation, the  
next time you write to this forum?

Thanks - SB

>
>
>
>
>
> ??Qosmio?? 
> ??___
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[Pw_forum] the wave function after scf calculation

[meisam aghtar]

Dear all
?how can i get the converged wave function?in a?scf calculation?
M.Aghtar
the?Msc student 
physics?department of Kashan university?


  
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