[Pw_forum] thin film

[Halima Zaari]

some one help me pleaze haw i can generate the atomic position and the
vaccumm  of thin film (monolayer bilayer ...)
thank you in advance

-- 
H.ZAARI
PhD Student in laboratory of magnetism and physics of high energy
Faculty of Sciences in Rabat - Morocco
Email:
* halimazaari at gmail.com *
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/b50b8131/attachment.html
 

[Pw_forum] Error in reading namelists

[Mitul Mundra]

I have a separate script in which I specify the number of number of
processors, the machine and all other relevant details and I submit the job
using qsub. The script seems to be working fine with another system having
64 Si atoms only but shows error with this system.

Thanks
Mitul


On Mon, Nov 18, 2013 at 6:52 PM, Paolo Giannozzi
wrote:

> On Sun, 2013-11-17 at 22:38 -0800, Mitul Mundra wrote:
>
>
> > I am trying to do NEB calculations but I keep on getting the following
> > error.
>
> >   from read_namelists  : error #18
> >   reading namelist system
>
> > My input file is like this.
>
> your input file is incomplete, you didn't specify the code version,
> the machine you use, on how many processors, how parallelized.
> Anyway, I do not see any problem in namelist "system".
>
> >   nat = 1729,
>
> Please note that if you want to run such a big job, you must be ready
> to solve problems of any kind.
>
> P.
> --
> Paolo Giannozzi, Dept. Chemistry&Physics&Environment,
> Univ. 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://pwscf.org/mailman/listinfo/pw_forum
>
------ next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/70bdc9f3/attachment.html
 

[Pw_forum] virtual.x and VCA problem

[Yue-Wen Fang]

Dear QEers?

I took many efforts to generate pseudo potentials(PPs) using ld1.x and mix
the PPs with virtual.x.  However, I  am still uncertain that whether
VCA(virtual crystal approximation) in Quantum Espresso can give us reliable
results. I hope experienced experts can tell me the reliability of it.

Additionally, when using mixed PPs generated by virtual.x, how to determine
the atomic weight? For example, if I mix N.pbe.UPF and O.pbe.UPF (ratio is
1:9) and then get a mixed PPs named NO.pbe.UPF, how to set the
ATOMIC_SPECIES in the input file?  Is the atomic weight 15.9994 or 14.0067
or (14.0067*0.9+15.9994*0.1)?

Any suggestion is appreciated. Thank you!




-- 

Yue-Wen FANG, PhD candidate
Key Laboratory of Polar Materials and Devices, Ministry of
Education<http://clpm.ecnu.edu.cn/>
East China Normal University  <http://english.ecnu.edu.cn/>
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/86bb4da1/attachment.html
 

[Pw_forum] thin film

[Sanjeev Gupta]

in addition, you can use many graphical packages or better way use xcrysden
and define the unit cell and then play around it. Further, I would like to
say read first solid state physics book for it.

bests
sanjeev


On Mon, Nov 18, 2013 at 5:12 PM, Yue-Wen Fang  wrote:

> You can try to use pwgui in Quantum Espresso. Personally, there are many
> ways to generate the positions.
> For example, you can write a fortran program to export them, or just write
> the positions based on the geometry.
>
> 2013/11/19 Halima Zaari 
>
>> some one help me pleaze haw i can generate the atomic position and the
>> vaccumm  of thin film (monolayer bilayer ...)
>> thank you in advance
>>
>> --
>> H.ZAARI
>> PhD Student in laboratory of magnetism and physics of high energy
>> Faculty of Sciences in Rabat - Morocco
>> Email:
>> * halimazaari at gmail.com *
>>
>> ___
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>
>
>
> --
>
> 
> Yue-Wen FANG, PhD candidate
> Key Laboratory of Polar Materials and Devices, Ministry of 
> Education<http://clpm.ecnu.edu.cn/>
> East China Normal University  <http://english.ecnu.edu.cn/>
>
>
>
>
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
With Best Regards,


Dr. Sanjeev Kumar Gupta
Fulbright Post-Doctoral Scholar
Dept. of Physics
Michigan Technological University
1400 Townsend Drive, Houghton
MI 49931, USA

-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/8e930212/attachment.html
 

[Pw_forum] Au (111) Surface Energy

[Nicola Marzari]

On 18/11/2013 15:30, Jack Davis wrote:
> Dear Ari,
>
> Any other papers you can provide relating to this problem would be extremely 
> useful. Thank you very much.
>
> Best Wishes,
> Jack Davis



Dear Jack,

the easiest would be looking at all the papers that cite the
Fiorentini-Methfessel paper. Also, google search Caspar Fall
PhD thesis at EPFL. Look also at Singh-Miller/Marzari PRB 2009.


nicola

--
Prof Nicola Marzari, Chair of Theory and Simulation of Materials, EPFL

[Pw_forum] Plotband.x error

[JdGa The Pro]

Dear Sir.

I'm a new user of the Quantum Espresso software. I have completed all the 
examples attached
to the software. However, when i use plotband.x on my graphite structure, i 
obtained this
error after put in the range parameters.
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0  0x7FD69BC27B07
#1  0x7FD69BC2810E
#2  0x7FD69AF2A25F
#3  0x7FD69BCDE2E0
#4  0x7FD69BCEB677
#5  0x420FF3
#6  0x41F59C
#7  0x7FD69AF16994
#8  0x41F5C8

Thanks for your attention.

Also, I attached the inputs and the outputs obtained using the comands pw.x and 
bands. x
  
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/a23b38e5/attachment.html
 
-- next part --
A non-text attachment was scrubbed...
Name: Grafito.bands.in
Type: application/octet-stream
Size: 5662 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/a23b38e5/attachment.obj
 
-- next part --
A non-text attachment was scrubbed...
Name: grafito.bands.out
Type: application/octet-stream
Size: 2745 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/a23b38e5/attachment-0001.obj
 
-- next part --
A non-text attachment was scrubbed...
Name: Grafito.band
Type: application/octet-stream
Size: 39229 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/a23b38e5/attachment-0002.obj
 
-- next part --
A non-text attachment was scrubbed...
Name: Grafito.scf.in
Type: application/octet-stream
Size: 5574 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/a23b38e5/attachment-0003.obj
 
-- next part --
A non-text attachment was scrubbed...
Name: Grafito.scf.out
Type: application/octet-stream
Size: 113310 bytes
Desc: not available
Url : 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/a23b38e5/attachment-0004.obj
 

[Pw_forum] Fwd: Energy of one metal atom

[Abhishek Mishra]

Dear all,

I wan to calculate energy of one Cu atom, what will be your suggestion?
calculating it by placing one copper atom in a bigbox or  calculating bulk
energy and dividing it by no of atoms(4)?, in later case then whether I
need to do something with cohesive energy as well?

Many thanks in advance.

Best regards,

Abhishek Mishra
TSU, JNCASR, Bangalore
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/c0dc043f/attachment.html
 

[Pw_forum] Imaginary Frequency

[Paolo Giannozzi]

It is impossible to answer on the basis of so little
information. It is difficult even in presence of all
needed information, since complete phonon dispersions
take so long to complete. 

Reminder: under some circumstances, phonons in v.5.0.2
may turn out to be incorrect. Use patched version 5.0.3.

P.


On Mon, 2013-11-18 at 09:44 +0900, Myungchul Jung wrote:
> Hi users,
>  
> In ABO3 structure, I consider an Osomate system.
> I used a PBE-pseudopotential.
> ecut = 40 Ry, ecutrho=400 Ry.
> First I used k-mesh 14*14*14 and q-mesh 2*2*2, then I got the
> imaginary freq.
> So, I used k-mesh 20*20*20 and q-mesh 2*2*2, then I didn't get the
> freq.
> But, when I used 4*4*4 q-mesh, I got a imaginary freq again.
> How I do to solve this problem?
>  
> Sincerely,
> Myung-Chul.
> ___
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum

-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] Au (111) Surface Energy

[Jack Davis]

Dear Ari,

Any other papers you can provide relating to this problem would be extremely 
useful. Thank you very much.

Best Wishes,
Jack Davis

On 15 Nov 2013, at 21:18, Ari P Seitsonen  wrote:


Dear Jack Davis,

 It is well known in the community that this is not a very accurate approach to 
calculate the surface energy, even if in principle correct (or, even the 
definition): You should at least make sure that the bulk is calculated along 
the (111) direction with the same k point sampling. Only if you are very well 
converged with the k point sampling in both the slab and bulk you might get a 
converged value. A classic article discussing this problem is

Vincenzo Fiorentini and M Methfessel 1996 J. Phys.: Condens. Matter 8 6525 
doi:10.1088/0953-8984/8/36/005
"Extracting convergent surface energies from slab calculations"

 I can also try to find some more recent references if you wish.

   Greetings from Zurich,

  apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
 Ari P Seitsonen / Ari.P.Seitsonen at iki.fi 
/ http://www.iki.fi/~apsi/
 Physikalisch-Chemisches Institut der Universitaet Zuerich
 Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935


On Fri, 15 Nov 2013, Jack Davis wrote:

Dear Forum,

I?m trying to calculate surface energies using PWscf, however, I am unsure of 
the methodology. To begin with we calculate the bulk energy of the FCC unit 
cell, using the attached input. We then calculate the energy of a 111 slab, 10 
layers thick with a 6 atom vacuum gap. The surface energy is then calculated as,

Surface energy = Energy of slab - (bulk energy * 10) / 2.

I think I am probably misunderstanding the energies PWscf is giving me. We?re 
getting some strange answers!

Thank you,
Jack Davis

School of Chemistry
University of Birmingham
___
Pw_forum mailing list
Pw_forum at pwscf.org
http://pwscf.org/mailman/listinfo/pw_forum

[Pw_forum] Fw: about Elishberg function

[Paolo Giannozzi]

On Sun, 2013-11-17 at 01:49 -0800, toktam morshedlo wrote:
> 
> I want to calculate Eliashberg function between two especial
> electronic bands.

you have to modify the phonon code in the part that calculates
the electron-phonon coefficients.

P.

-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] Error in reading namelists

[Paolo Giannozzi]

On Sun, 2013-11-17 at 22:38 -0800, Mitul Mundra wrote:


> I am trying to do NEB calculations but I keep on getting the following
> error.

>   from read_namelists  : error #18
>   reading namelist system 

> My input file is like this.

your input file is incomplete, you didn't specify the code version,
the machine you use, on how many processors, how parallelized.
Anyway, I do not see any problem in namelist "system". 

>   nat = 1729,

Please note that if you want to run such a big job, you must be ready 
to solve problems of any kind.

P.
-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] virtual.x and VCA problem

[Paolo Giannozzi]

On Mon, 2013-11-18 at 19:03 +0800, Yue-Wen Fang wrote:

> Additionally, when using mixed PPs generated by virtual.x, 
> how to determine the atomic weight? 

atomic weights are used only for molecular dynamics
and phonon calculations. Unless you want to perform
such calculations using VCA (likely not a good idea)
you may choose whatever atomic weight you like

P.
-- 
Paolo Giannozzi, Dept. Chemistry&Physics&Environment, 
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222 

[Pw_forum] TPSS Pseudopotentials, too many bands are not converged

[Kayahan Saritas]

Dear PWSCF users,

I am trying to do ground state relaxation calculations on dihydroazulene with 
TPSS functional.I started with atomic coordinates from PBE calculations and 
used several mixing parameters with increasing cutoff energy values (up to 100 
Ry), but still I receive ?too many bands are not converged? error according to 
the given advice in prior posts. I changed nbds parameter, I have 102 
electrons, but it wasn?t also very useful.  I also tried forcing several 
functional pseudo potentials, except meta-gga unfortunately, to see if the 
error changes but it was of no use. When I check the manual, it says the 
current atomic code in current Espresso distribution does not include TPSS PP 
generation functionalities. If you could share with me that old version which 
is capable of generating TPSS PP? s it would be great. If you think that there 
might be another problem, I also include my input and output file here, any 
help would be much appreciated.

Thanks,
Kayahan

Input file:
https://docs.google.com/document/d/1T5NbRu7p3JV8O9r6sSrT6oub1waid2azEYAsoMBvyxM/edit

Output file:
https://docs.google.com/document/d/1_gGGFsGlaUDr661Cm38D_wXbz2vCOCiJRMDIeOJhP8E/edit

Saritas Kayahan
Research Assistant
MIT
Grossman Group
Office: 13-4069
Cell: +1-617-955-3981
Office: +1-617-258-8741
Email: kayahan at mit.edu


-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/27e90c3c/attachment.html
 

[Pw_forum] Imaginary Frequency

[Myungchul Jung]

Hi users,

In ABO3 structure, I consider an Osomate system.
I used a PBE-pseudopotential.
ecut = 40 Ry, ecutrho=400 Ry.
First I used k-mesh 14*14*14 and q-mesh 2*2*2, then I got the imaginary
freq.
So, I used k-mesh 20*20*20 and q-mesh 2*2*2, then I didn't get the freq.
But, when I used 4*4*4 q-mesh, I got a imaginary freq again.
How I do to solve this problem?

Sincerely,
Myung-Chul.
-- next part --
An HTML attachment was scrubbed...
URL: 
http://pwscf.org/pipermail/pw_forum/attachments/20131118/80d7c28b/attachment.html