The ABINIT Users Mailing List ( CLOSED )

[Josef Zwanziger <jzwanzig@gmail.com>]

Visualizing is easy to do at the point when you make the pseudos, but
hard to do after they're made. Basically you would have to write a
program (in python or whatever) to extract the various quantities from
the files, make ascii tables, and plot them. With the PAW data sets
this isn't too hard because they are saved in a well-labeled format,
but the FHI style format is hard to read. It would be much much more
efficient for you to install the fhi software locally, which comes
with a really excellent tutorial by the way, and then run the relevant
input files through it. It will use xmgrace (or gnuplot, I don't quite
remember which) to make really nice plots of the various interesting
quantities, such as the pseudowavefunctions and log derivatives, as it
makes the peudopotential files.

On Tue, Jan 27, 2009 at 8:43 PM, Anurag Chaudhry
<anuragchaudhry@yahoo.co.uk> wrote:
> Hello,
>
> I have a follow up question on the discussion on pseudopotentials.  For the
> TM pseudopotentials (ftp://ftp.abinit.org/pub/abinitio/Psps/LDA_TM.psps/)
> generated by A.Khein and D.C. Allan   how can we plot/visualize them ?
>
> like for example for Ce the file looks like as follows with the entire row
> of data similar.
>
> Troullier-Martins psp for element  Ce        Thu Oct 27 17:46:26 EDT 1994
>   58.00000   4.00000    940714                zatom, zion, pspdat
>     1    1    3    0      2001    .00000
> pspcod,pspxc,lmax,lloc,mmax,r2well
>     0   2.878   5.676    0   3.3687586        l,e99.0,e99.9,nproj,rcpsp
>     .00000000    .0000000000    .0000000000    .00000000
> rms,ekb1,ekb2,epsatm
>     1   2.235   3.818    1   3.8173093
>  l,e99.0,e99.9,nproj,rcpsp
>     .00000000    .0000000000    .0000000000    .00000000
> rms,ekb1,ekb2,epsatm
>     2   4.730   6.452    1   2.6899998        l,e99.0,e99.9,nproj,rcpsp
>     .00000000    .0000000000    .0000000000    .00000000
> rms,ekb1,ekb2,epsatm
>     3  17.890  22.471    1   2.9729140        l,e99.0,e99.9,nproj,rcpsp
>     .00000000    .0000000000    .0000000000    .00000000
> rms,ekb1,ekb2,epsatm
>     4.29523888345602     .03353069390661    2.31873700049175
> rchrg,fchrg,qchrg
>     0 =l for Troullier-Martins pseudopotential
>   -8.1749183755652566E-01  -8.1749183755652566E-01  -8.1749183755652566E-01
>   -8.1749183755652555E-01  -8.1749183755652566E-01  -8.1749183755652544E-01
>   -8.1749183755652532E-01  -8.1749183755652521E-01  -8.1749183755652521E-01
>   -8.1749183755652510E-01  -8.1749183755652499E-01  -8.1749183755652499E-01
> .................
>   -8.1749183755652477E-01  -8.1749183755652455E-01
>  -8.1749183755652433E-01
>
> thanks,
> Anurag
>
> ________________________________
> From: matthieu verstraete <matthieu.jean.verstraete@gmail.com>
> To: forum@abinit.org
> Sent: Monday, 26 January, 2009 9:28:25
> Subject: Re: [abinit-forum] pseudopotential expression
>
> For the TM FHI potentials, Joe is absolutely correct. In some cases the new
> version of the fhi code (which is not the one I used to make the .fhi
> initially) does not allow you to reconstruct the exact same pseudopotential
> which is in the web site. This is unfortunate, and was discussed a few years
> ago on the forum. However, the occupations for the reference configuration
> are certainly those given in the .ini files. The cutoff radii are probably
> valid as well.
>
> For other types of pseudopotentials, you have to check the cited papers
> (HGH, GTH etc, Teter maybe). Most of them give case-by-case configurations,
> but some may not be that precise. Some of the other potentials have
> configurations in the header of the online files.
>
> Matthieu
>
> On Mon, Jan 26, 2009 at 5:37 PM, Josef Zwanziger <jzwanzig@gmail.com> wrote:
>>
>> Oh, I see, you want to know which states are being used for valence
>> and which for core. That detail is best found in the input files used
>> to make the pseudos. For the TM LDA files available on the abinit web
>> site (see the page
>> http://www.abinit.org/Psps/?text=../Psps/LDA_FHI/fhi) you find at the
>> top a periodic table of the pseudopotential files, and then another
>> periodic table of the input files. If you open an input file say for
>> Carbon, you will see at the top the line
>>
>> 6.00 1 2 8 0.00 : z nc nv
>>
>> which means nuclear charge 6, 1 core level, 2 valence levels, because
>> this pseudo was made with 1s2 core and 2s2,2p2 valence.
>>
>> Hope this helps!
>>
>> Joe
>>
>> On Mon, Jan 26, 2009 at 11:57 AM, Souraya Goumri-Said
>> <Souraya.Goumri-Said@fundp.ac.be> wrote:
>> > I mean by the "expression"  the electronic configuration considered in
>> > the
>> > psp generation, those ( between (.....) such as :
>> >
>> > Boron (2s2 , 2p1 ),
>> > nitrogen (2s 2, 2p3 )
>> >  magnesium (3s 2)
>> >
>> >
>> > When I open psp file, I can't find this detail ???
>> >
>> > thank's again;
>> >
>> > Souraya,
>> >
>> >
>> >
>> >
>> > At 16:50 26/01/2009, you wrote:
>> >
>> > What do you mean by "expression"? Do you mean the input file used to
>> > generate it? Or do you mean a mathematical description of the
>> > pseudopotential generating process?
>> >
>> > On Mon, Jan 26, 2009 at 11:41 AM, Souraya Goumri-Said
>> > <Souraya.Goumri-Said@fundp.ac.be> wrote:
>> >> Dear ABINIT users,
>> >>
>> >> I am searching in pseudopotential home page files ( under
>> >> http://www.abinit.org/Psps/?text=psps) for pseudopotential expression.
>> >> For
>> >> example for Ti (3s23p64s03d2 ) but when I open for any element in TM
>> >> psp (
>> >> http://www.abinit.org/Psps/?text=../Psps/LDA_TM/lda) , for example O :
>> >>
>> >> Troullier-Martins psp for element  B         Thu Oct 27 17:29:24 EDT
>> >> 1994
>> >>    5.00000   3.00000    940714                zatom, zion, pspdat
>> >>     1    1    1    1      2001    .00000
>> >> pspcod,pspxc,lmax,lloc,mmax,r2well
>> >>     0   8.313  21.401    1   1.5924135        l,e99.0,e99.9,nproj,rcpsp
>> >>     .00000000    .0000000000    .0000000000    .00000000
>> >> rms,ekb1,ekb2,epsatm
>> >>     1  11.531  17.234    0   1.5924135        l,e99.0,e99.9,nproj,rcpsp
>> >>     .00000000    .0000000000    .0000000000    .00000000
>> >> rms,ekb1,ekb2,epsatm
>> >>     1.10004537463277     .35216853368804     .40909985967175
>> >> rchrg,fchrg,qchrg
>> >>     0 =l for Troullier-Martins pseudopotential
>> >>
>> >>
>> >> My question, where I can find the expression of any psp ?
>> >>
>> >>
>> >>
>> >> Cordialement,
>> >> Sincerely yours,
>> >>
>> >> ====================================
>> >> Dr. Souraya Goumri-Said
>> >> Centre de recherche en Physique de la Matière et du Rayonnement (PMR)
>> >> Laboratoire de Physique du Solide
>> >> FacultÃ(c)s Universitaires Notre-Dame de la Paix
>> >> Rue de Bruxelles 61 - B - 5000 Namur
>> >> Tel : +32(0)81 72 47 01
>> >> Fax : +32(0)81 72 47 10
>> >> email : Souraya.Goumri-Said@fundp.ac.be
>> >>
>> >
>> >
>> >
>> > --
>> > Josef W. Zwanziger
>> > Professor of Chemistry
>> > Canada Research Chair in NMR Studies of Materials
>> > Director, Atlantic Region Magnetic Resonance Centre
>> > Dalhousie University
>> > Halifax, NS B3H 4J3 Canada
>> > tel: +1 (902) 494-1960
>> > fax: +1 (902) 494-1867
>> > web: http://jwz.chem.dal.ca
>> > jzwanzig@gmail.com, jzwanzig@dal.ca
>> >
>> > Cordialement,
>> > Sincerely yours,
>> >
>> > ====================================
>> > Dr. Souraya Goumri-Said
>> > Centre de recherche en Physique de la Matière et du Rayonnement (PMR)
>> > Laboratoire de Physique du Solide
>> > Facultés Universitaires Notre-Dame de la Paix
>> > Rue de Bruxelles 61 - B - 5000 Namur
>> > Tel : +32(0)81 72 47 01
>> > Fax : +32(0)81 72 47 10
>> > email : Souraya.Goumri-Said@fundp.ac.be
>> >
>>
>>
>>
>> --
>> Josef W. Zwanziger
>> Professor of Chemistry
>> Canada Research Chair in NMR Studies of Materials
>> Director, Atlantic Region Magnetic Resonance Centre
>> Dalhousie University
>> Halifax, NS B3H 4J3 Canada
>> tel: +1 (902) 494-1960
>> fax: +1 (902) 494-1867
>> web: http://jwz.chem.dal.ca
>> jzwanzig@gmail.com, jzwanzig@dal.ca
>>
>
>
>
> --
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Dr. Matthieu Verstraete
>
> European Theoretical Spectroscopy Facility (ETSF)
> Dpto. Fisica de Materiales,
> U. del Pais Vasco,
> Centro Joxe Mari Korta, Av. de Tolosa, 72,   Phone: +34-943018393
> E-20018 Donostia-San Sebastian, Spain        Fax  : +34-943018390
>
> Mail : matthieu.jean.verstraete@gmail.com
> http://www-users.york.ac.uk/~mjv500
>
>



-- 
Josef W. Zwanziger
Professor of Chemistry
Canada Research Chair in NMR Studies of Materials
Director, Atlantic Region Magnetic Resonance Centre
Dalhousie University
Halifax, NS B3H 4J3 Canada
tel: +1 (902) 494-1960
fax: +1 (902) 494-1867
web: http://jwz.chem.dal.ca
jzwanzig@gmail.com, jzwanzig@dal.ca