Re: [Pw_forum] XSpectra and US or PAW pseudos?
it?
>>>
>>> Thanks
>>>
>>> Mojtaba Mirseraji
>>> Ph.D. Candidate
>>> Department of Physics
>>> Arak Univ.
>>> IRAN
>>>
>>>
>>> On 8/25/15, Bahad?r salmankurt <bsalmank...@gmail.com> wrote:
>>>> Dear Mojtaba Mirseraji
>>>>
>>>> please add these line to .bashrc
>>>>
>>>> export PATH=$PATH:$Elas-tic:.
>>>>
>>>> export BERRYPI_PATH=$Elas-tic/SRC_BerryPI/BerryPI
>>>>
>>>> export BERRYPI_PYTHON=/usr/bin/python3.2 ===> change version according
>>> to
>>>> yours.
>>>>
>>>> alias berrypi="${BERRYPI_PYTHON} ${BERRYPI_PATH}/berrypi"
>>>>
>>>>
>>>> if you overcome this problem then another problem occur -if happen -,
>>> type
>>>> this to command line
>>>>
>>>>
>>>> *sudo apt-get install python-numpy python-scipy python-matplotlib
>>>> ipython
>>>> ipython-notebook python-pandas python-sympy python-nose*
>>>>
>>>>
>>>> Bests
>>>>
>>>> Bahadir
>>>>
>>>> Sakarya University, TURKEY
>>>>
>>>> 2015-08-25 19:27 GMT+03:00 Mojtaba Mirseraji <quantum.pw...@gmail.com>:
>>>>
>>>>> Dear All
>>>>>
>>>>> I run ./sgroup successfully but when I want to use:
>>>>> ./Elastic_Setup
>>>>>
>>>>> I face to this error:
>>>>>
>>>>> " Oops sh: 1: Elastic_Setup_Espresso: not found."
>>>>>
>>>>> but I see the code of Elastic_Setup_Espresso
>>>>>
>>>>> I do not know why this problem happens!!!
>>>>> Please help me
>>>>> you can find this code:
>>>>> http://exciting-code.org/elastic
>>>>>
>>>>>
>>>>> Regards
>>>>>
>>>>> Mojtaba Mirseraji
>>>>> Ph.D. Candidate
>>>>> Department of Physics
>>>>> Arak Univ.
>>>>> IRAN
>>>>> ___
>>>>> Pw_forum mailing list
>>>>> Pw_forum@pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>>
>>> ___
>>> Pw_forum mailing list
>>> Pw_forum@pwscf.org
>>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> --
>
> Message: 7
> Date: Fri, 28 Aug 2015 18:31:03 +0200
> From: Delphine Cabaret <delphine.caba...@impmc.upmc.fr>
> Subject: Re: [Pw_forum] XSpectra and US or PAW pseudos?
> To: PWSCF Forum <pw_forum@pwscf.org>
> Message-ID: <55e08cc7.5010...@impmc.upmc.fr>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Hello Adrian
>
> You are right about the contradiction because I wrote v5.0.2 twice in
> my email and I apologize for it (it was late). To be clear, it is the
> version v.5.2.0. that contains a bug. Thus it is better to use the v5.0.2.
>
> Regards
>
> Delphine
>
> Le 28/08/2015 12:34, Adrian H?hn a ?crit :
>> Hello Delphine,
>>
>> thanks for your quick reply! This seems to be a contradiction to my
>> observations. Maybe I did not write this in detail, but I was only able
>> to get sensible results when calculating diamond USPP spectra with
>> v.5.0.2. The same setup fails with the recent v.5.2.0. To be more
>> specific: Both PWscf and the XSspectra calculations run on both
>> versions, but the data from "xanes.dat" is useless on the recent 5.2.0.
>> I uploaded the setups.
>> http://www.file-upload.net/download-10870211/diamondh_uspp_5.0.2.tar.gz.html
>> http://www.file-upload.net/download-10870213/diamondh_uspp_5.2.0.tar.gz.html
>>
>> Concerning my problem with periclase or magnesium pseudopotentials (my
>> last trials are with NC): do you think this could also trigger the
>> segmentation fault?
>> I recompiled QE 5.0.2 without parallelization (./configure
>> --disable-parallel) but this does not make any difference.
>>
>> At I deeper look I can see, that the code fails at the same point,
>> perhaps when "paw_recon(xiabs)" is accessed.
>> espresso-5.0.2/XSpectra/src/xspectra.f90:461 or
>> espresso-5.2.0/XSpectra/src/xspectra.f90:592
>> [code]
>> 456 !
>> $$$
[Pw_forum] EELNE Spectra
> > > -- > > Message: 1 > Date: Wed, 12 Dec 2012 10:00:45 -0800 > From: Sanjeev Gupta > Subject: [Pw_forum] EELNE Spectra > To: PWSCF Forum > Message-ID: > > Content-Type: text/plain; charset="iso-8859-1" > > Dear PWSCF users > > I am interested to calculated the Electron Energy Loss Near-Edge Fine > spectra. I would like to know weather PWSCF can calculate? > suggest. > > > > Best Regards > Sanjeev > Dear Sanjeev, in the limit of small exchanged momentum, in the dipolar approximation and for a K-edge, you can use XSpectra code. XSpectra code calculates XAS spectra at the K-edge. However, under the assumptions mentioned above, EELS = XAS with epsilon (polarization of the X-ray beam) exchanged with k (exchanged momentum in eels). Thus you can run xspectra with a given epsilon and you will get the eels spectrum. This is not true for higher multipoles. M. So you > > -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] XSpectra hybrid functional
Le 24/10/12 12:00, pw_forum-request at pwscf.org a ?crit : >It is possible indeed, in the sense that the XSPECTRA code does not stop >complaining if you perform >the calculation starting from an electronic density calculated by using hybrid >functionals (or >DFT+U). But the XSPECTRA code has not a calculation kernel including EXX >terms, as just pointed out >by Matteo Calandra. Thus: Not exactly. In the case of DFT+U, the lanczos is performed, as it must be, with the U term included in the hamiltonian. So the Hamiltonian H used in XSpectra to perform H|psi> is the same used to generate the charge density. This is of course what must be done. So everything is consistent with DFT+U. If you take the charge density calculated with hybrids and calculate the H|psi> without hybrid I do not think that the result is very meaningful... M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] XSpectre hybrid functional
>Dear All, >I am interested in using XSpectra in QE to do some hybrid >functional XANES calculations. Some hybrid functionals such as B3LYP, HSE, >and PBE0 have been implemented in QE and I am wondering if these >functionals can be used to do XANES calculations? Thanks. Currently hybrid funtionals are not implemented. I planned to do it as soon as I have time (and I do not have a lot of time, unfortunately). M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] xspectra - forrtl: severe (43)
Le 23/10/12 10:48, pw_forum-request at pwscf.org a ?crit : > Dear QE Users, > I started to work with ?xspectra.x? sub-program. After compilation of > ?xspectra? subroutine, I tested accuracy of the program by testing > ?Diamond and NiO? examples (with and without core-hole effect). I didn?t > have any errors/problems with the examples. Next, I did a test for CdO > (unit cell; without CH effect) which worked properly, with no > errors. > As a next step, I prepared test-?run? file for CdO supercell. After ?scf? > cycle the next error appeared: Dear Iraida, the code tries to read a file that is not there. Do all of your pseudos has gipaw reconstruction ? M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] ele phonon coupling at the gamma point
>
>
> Dear all,I am trying to do el-ph calculations only at the Gamma point for
> graphene (as I want to compare it to another system where the calculations
> are only feasible at the Gamma point). However the values I am getting for
> lambda for graphene AT THE GAMMA POINT are :
> degauss lambda 0.005 13.442600 0.0152.303600 0.020
> 1.756000 0.0251.436000 0.0301.228800 0.0351.085800
> 0.0400.983000 0.0450.906400 0.0500.847800I am using
> a 90 x90 x1 grid (in scf) for graphene and the ph file has only one point
> nq1=0 nq2=0, nq3=0 (the Gamma point).
> It is already known that lambda for graphene is ~0.02. (1) Do the above
> results mean that one cannot calculate el-ph coefficients unless on a grid of
> phonons and then are the calculations -at the Gamma point ONLY- useless and
> unexact?
> (2) or does this mean that the results did not converge due to a small k-mesh
> in the scf calculations (90x90x1) and I need to increase it to say 400x400x1?
> Any suggestions of any kind would also be ahighly appreciated.
> Thanks for your help
> Elie MUniversity of NottsNG7 2RDUK
Dear Elie,
as it is well known, the electron-phonon coupling (lambda) and the
phonon linewidth (gamma) for an optical mode diverge at zone center, at
least for what concerns the equation implemented in QE.
So it is pointless to consider more k-points and smaller smearings.
The issue is of course different if you consider
the electron-phonon matrix element ( |g_{kn,k+qm}^{nu}|^2 ) that is an
object well defined at any q in the BZ for an optical mode.
You can have more details on the behaviour of the lambda or of the
phonon linewidth in PRB 71, 064501 (2005) .
All the best,
M.
--
* * * *
Matteo Calandra, Directeur de Recherche (DR2)
Institut de Mineralogie et de Physique des Milieux Condenses de Paris
Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115
4 Place Jussieu, 75252 Paris Cedex 05 France
Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85
http://www.impmc.jussieu.fr/~calandra
[Pw_forum] (Niharika Joshi)
Le 24/01/12 09:33, pw_forum-request at pwscf.org a ?crit : > -- > > Message: 2 > Date: Tue, 24 Jan 2012 11:49:00 +0530 (IST) > From: Niharika Joshi > Subject: [Pw_forum] Occupied states in XAS > To: "pw_forum at pwscf.org" > Message-ID:<1327385940.93549.YahooMailNeo at web95709.mail.in.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello, > > In the xspectra calculation, the option 'cut_occ_states=.false.' will include > the occupied states in XAS. > Why should one consider occupied states in absorption spectra because the > transitions are only to empty states. Or have understood it wrong? > ?-Niharika Joshi Dear Niharika, of course in XAS only empty states are measured. However plotting occupied states could be useful for low energy features (pre-edge region). When for example there is not a clear large gap, it can be difficult to isolate empty from occupied states. This is the case in metals or small gap systems. So it can be useful to look at the full spectrum and see where the Fermi level is located. M. > (Project student, Indian Institute of Science Education and Research, Pune, > India) > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20120124/bccced8d/attachment-0001.htm > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 55, Issue 39 > -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] pseudopotential (Hanghui Chen)
Le 01/12/11 09:38, pw_forum-request at pwscf.org a ?crit : > > Message: 2 > Date: Wed, 30 Nov 2011 23:40:19 -0500 > From: Hanghui Chen > Subject: [Pw_forum] pseudopotential > To: pw_forum at pwscf.org > Message-ID: >
[Pw_forum] problem in xspectra calculations
> Message: 4 > Date: Tue, 11 Oct 2011 15:01:33 +0530 (IST) > From: Niharika Joshi > Subject: Re: [Pw_forum] problem in xspectra calculations > To: PWSCF Forum > Message-ID: > <1318325493.18035.YahooMailClassic at web95715.mail.in.yahoo.com> > Content-Type: text/plain; charset="iso-8859-1" > > Hello Paolo Sir, > Thank you for your reply. > I tried running the xanes calculation after making the change in > xspectra.f90. But it is still giving me the same message 'Could not find the > element? C in the table of K edge energies!' at the end and leaving the > output file incomplete. > For some reason, the condition for 'if-loop' in mygetK.f90 is not getting > satisfied and thus it is not getting executed. I wrote the variables sym and > seuilK_tab(6) . For both variables it writes 'C' but does not enter the > if-loop. > -Niharika Joshi > (project student, IISER Pune) Dear Niharita, which compiler/Machine are you using ? It seems it treats in a strange way string variables. Moreover, are you using the pseudo of the example for Carbon or another one ? You can try the following two options: 1) in ligne 66 in mygetK.f90 change line if(sym.eq.seuilK_tab(i)%name) then in if(sym.eq.trim(adjustl(seuilK_tab(i)%name))) then 2) if it doesn't work, then replace in xspectra.f90 all the lines with (two lines) of e_1s=mygetK(upf(xiabs)%psd) with the actual value of the Carbon K-edge energy, namely with e_1s=284.2 All the best, M. -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] XSpectra calculation error
um simulation of materials; please cite >> "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009); >> URL http://www.quantum-espresso.org;, >> in publications or presentations arising from this work. More details at >> http://www.quantum-espresso.org/wiki/index.php/Citing_Quantum-ESPRESSO >> >>Info: using nr1, nr2, nr3 values from input >> >>Info: using nr1s, nr2s, nr3s values from input >> >> G-vector sticks info >> >> sticks: dense smooth PW G-vecs:dense smooth PW >> Sum 163 163 61 1459 1459 339 >> >> Segmentation fault >> >> any help would be appreciated. >> best, >> Karthik >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum > > --- > Changru Ma > SISSA& Theory at Elettra group > email: crma at sissa.it > tel: +39 040 378 7870 > http://www.sissa.it/~crma > --- > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110905/9d133c90/attachment.htm > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 51, Issue 9 > *** -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] XANES SiO2
t;>> puzzling. >>> Specifically, plasma frequency given in the output of epsilon.x is dependent >>> on the input parameters: >>> <1>. intrasmear=0, wmax=20d0 --> The bulk xx plasmon frequency [eV] >>> is: >>> 14.877926200 >>> <2>. intrasmear=0, wmax=10d0 --> The bulk xx plasmon frequency [eV] >>> is: >>> 7.625822195 >>> <3>. intrasmear=0, wmax=6d0 --> The bulk xx plasmon frequency [eV] >>> is: >>> 3.156554381 >>> <4>. intrasmear=0.1, wmax=20d0 --> The bulk xx plasmon frequency [eV] >>> is: >>> 15.766403193 >>> <5>. intrasmear=0.1, wmax=10d0 --> The bulk xx plasmon frequency [eV] >>> is: >>> 9.322251787 >>> <6>. intrasmear=0.1, wmax=20d0 --> The bulk xx plasmon frequency [eV] >>> is: >>> 6.263713572 >>> However, none of these values is the one got by fitting the results using >>> Drude model [ 1 - omega_p^2/(omega^2+i*omega*gamma), gamma is the intrasmear >>> here ]. By fitting the results using Drude model, I get omega_p=5.528769eV, >>> for all the cases above (<1>~<6>). But this omega_p is far from the >>> experimental value (~9 eV)! What's wrong? And what are the meanings of the >>> values given in<1>~<6> ? >>> >>>How can I get more accurate results like the ones from wien2k? >>>Please help me if you know something about this, thanks in advance! >>> >>> Best regards! >>> >>> Liu Guibin >>> Postdoctoral Fellow, >>> Department of Physics, >>> The University of Hong Kong >>> gbliu at hku.hk >>> >>> >>> >>> >>> >>> >>> ___ >>> Pw_forum mailing list >>> Pw_forum at pwscf.org >>> http://www.democritos.it/mailman/listinfo/pw_forum >>> >>> > > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20110708/07a52d63/attachment.htm > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 49, Issue 20 > -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] SiO2 xanes calculation
>Message: 3 >Date: Wed, 06 Jul 2011 18:27:57 -0400 >From: >Subject: [Pw_forum] SiO2 xanes calculation >To: pw_forum at pwscf.org >Message-ID: >Content-Type: text/plain; charset="utf-8" > >Hi, > >I'm trying to repeat the ultrasoft core-hole calculation of the Si >K-edge >in Matteo's paper: > >"First-principles calculations of x-ray absorption in a scheme >based on ultrasoft pseudopotentials: From alpha-quartz to >high-Tc compounds" >I haved used the same parameters given in that article (cell size, >cutoff >energies, kpoints) but the spectrum that I get does not at all look >right. >Is it possible that this discrepancy is due to the choice of >pseudopotentials? For the absorbing atom I am using Dear Max, the pseudo you use are correct, however this is not the case for the k-points in your Xanes calculation. In the paper it is stated that you need "the Lanczos method was performed using a centered 3x3x3 k-points grid of the 72 atoms supercell." (see just below Eq. 27). The second thing is that in an insulator, there is no Fermi level. Are you sure you're cutting eliminated the occupied states at the right energy position ? Can you try yo see if you reproduce the results of the QE XSpectra example directory ? all the best, Matteo -- * * * * Matteo Calandra, Directeur de Recherche (DR2) Institut de Mineralogie et de Physique des Milieux Condenses de Paris Universite Pierre et Marie Curie, tour 23, 3eme etage, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] XSpectra can not run
> hi, Paolo, > Thank Matteo and you very much! Well, I got some similar reading > error when I tried to do XSpectra calculation with my own input file. > Could you please see the post > http://www.democritos.it/pipermail/pw_forum/2011-April/020020.html > for me (I apologize if you've already seen it)? Thank you very much! > best wishes > Yu Zhang > Dear Yu Zhang, I think the problem is that some of your pseudopotentials do not have gipaw reconstruction inside. In principle this is needed only for the absorbing atom, but for the moment the code requires that all the pseudo do have gipaw reconstruction. I have to modify this as soon as I have some time. Th second problem is that xspectra does not work with the Gamma only version of the code. So you should run both the scf and xspectra not with K_POINTS gamma but with K_POINTS automatic 1 1 1 0 0 0 It should then work. M. > On 04/08/2011 12:18, Paolo Giannozzi wrote: >> On Apr 8, 2011, at 20:49 , Yu Zhang wrote: >> >>> This really solves my problem! Thank you very much. >> you should thank Matteo Calandra, not me >> >>> Could you please explain briefly what the cause of the problem is? >> the problem is that some recent changes to the initialization of FFT >> grids, G-vectors, and other basic stuff, had not been propagated >> to that particular routine. I had forgotten that XSpectra uses a >> different routine to read the data file from all other QE codes. >> Just an overlook. >> >> Paolo >> --- >> Paolo Giannozzi, Dept of Chemistry, >> 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://www.democritos.it/mailman/listinfo/pw_forum >> > > > > -- > > Message: 2 > Date: Mon, 11 Apr 2011 17:15:33 -0500 > From: "Nichols A. Romero" > Subject: Re: [Pw_forum] I/O performance on BG/P systems > To: PWSCF Forum > Cc: Gabriele Sclauzero > Message-ID:
[Pw_forum] XSpectra on graphite slab
Dear Alain, as you can read in the manual of the XSPECTRA code, xiabs must be the type of the absorbing atom. In your case, as you put the Ch as the second atom type, then your xiabs must be 2. For what concerns the london option this has never been tested. I have no idea where the DFT-D part of the code is and how it interact with the rest. So it will probably not work. But this is an independent problem. Finally note that here http://cdsagenda5.ictp.it/full_display.php?agenda_id=3218 you can find my lectures on xspectra in which the case of diamond is treated. Convergence with respect to the cell size is very pathological in diamond. All the best, M. Quoting 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. Re: XSpectra on graphite slab (Paolo Giannozzi) >2. Re: norm conserving Ti pseudopotential (Nicola Marzari) >3. Re: XSpectra on graphite slab (Alain Allouche) > > > -- > > Message: 1 > Date: Wed, 16 Mar 2011 23:12:12 +0100 > From: Paolo Giannozzi > Subject: Re: [Pw_forum] XSpectra on graphite slab > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed > > On Mar 16, 2011, at 16:22 , Alain Allouche wrote: > >> Can somebody explain me the curious behavior of pw.x accepting Ch >> on diamond and not on graphite, and this "Wrong xiabs!!!" ?? > > > I'll do half of the job. It is the "london" option that makes the > difference. > Actually "Ch" is not acceptable syntax, or, more exactly: function > "atomic_number" accepts "X", "Xn", n=0,...,9, "X-*", "X_*", where X > is any atomic symbol. "Xh" confuses it. Since such routine is not > actually > called, except in some special cases (DFT-D is one such cases), this has > gine unnoticed until now > > P. > --- > Paolo Giannozzi, Dept of Chemistry, > Univ. Udine, via delle Scienze 208, 33100 Udine, Italy > Phone +39-0432-558216, fax +39-0432-558222 > > > > > > > -- > > Message: 2 > Date: Wed, 16 Mar 2011 22:49:17 + > From: Nicola Marzari > Subject: Re: [Pw_forum] norm conserving Ti pseudopotential > To: PWSCF Forum > Cc: Paolo Giannozzi > Message-ID: <4D813E6D.4040001 at materials.ox.ac.uk> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > On 3/16/11 6:15 PM, Paolo Giannozzi wrote: >> >> On Mar 16, 2011, at 19:01 , Nicola Marzari wrote: >> >>> Worse case scenario: download/compile the fritz-haber pseudopotential >>> code, generate the troullier-martins Ti there, and convert it to UPF >>> with the fhi2upf tool in the upftools directory of Q-E. >> >> this can be done directly with the "atomic" code in QE. Generating a >> single-channel >> norm-conserving PP without semi-core states is trivial and well >> documented. >> > > > I agree - one still needs to choose core radii wisely, and avoid > ghost states - so one could use those chosen by the fhi code. I also > recall that Philippe Gosez, in his PhD thesis, had good/tested values - > maybe one could ask him what he used. > > Thanks to Derek for pointing out the pseudo vault, as well. > > nicola > > -- > Prof Nicola MarzariDepartment of MaterialsUniversity of Oxford > Chair of Materials Modelling Director, Materials Modelling Laboratory > nicola.marzari at materials.ox.ac.uk http://mml.materials.ox.ac.uk/NM > > > -- > > Message: 3 > Date: Thu, 17 Mar 2011 08:37:59 +0100 > From: Alain Allouche > Subject: Re: [Pw_forum] XSpectra on graphite slab > To: PWSCF Forum > Message-ID: > Content-Type: text/plain; charset=ISO-8859-1; format=flowed; delsp=yes > > Merci Paolo, I should have though by myself... But even without > London, after the right results of pw, XSpectra gives the message > which I had not with diamondh > > - > --- Polarisation and k vector [cartesian coordinates] > xepsilon(:)= 1. 0. 0. > xkvec(:)= 1. 0. 0. > > % > % > from main program : error #63 > Wrong xiabs!!! > % > % > > stopping ... > > using these data: > > _xspectra > calculation='fermi_level', > prefix='graphite', >
[Pw_forum] Help XSPectra calculation
Dear Suman Dhayal, fro; the output of your script it seems to me that you are not running at all the XSpectra example but the general QE example. And the segmentation fault that you find has little do to with xspectrq but this is connected with the bands.x file. The XSpectra examples are in another directory. M. >> >> >> > > -- > > Message: 8 > Date: Mon, 15 Nov 2010 23:58:25 -0600 > From: Suman Dhayal > Subject: [Pw_forum] Help! > To: PWSCF Forum > Message-ID: > <AANLkTini_xSF1buwg3VFTufuGE8D+jM-si+7YaU39vKB at mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > hi, > > I configured and compiled the code but when I run example01, it runs for Si > but not for Al. It gives me a segmentation fault error and then says exit > status as follows: > > This example shows how to use pw.x to calculate the total energy and > the band structure of four simple systems: Si, Al, Cu, Ni. > > executables directory: /home/suman/Diff_folders/Diff_ > Codes/espresso-4.2.1/bin > pseudo directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/espresso-4.2.1/pseudo > temporary directory: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file > checking that needed directories and files exist... done > > running pw.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/pw.x > running bands.x as: > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/bin/bands.x > > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Si... done > running the band-structure calculation for Si... done > running the symmetry analysis for Si bands...Segmentation fault > done > cleaning > /home/suman/Diff_folders/Diff_Codes/espresso-4.2.1/Temp_data_file... done > running the scf calculation for Al...Segmentation fault > Error condition encountered during test: exit status = 139 > Aborting > > Thanks for the help, > > Harli > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101115/0b3385a5/attachment.htm > > > -- > > ___ > Pw_forum mailing list > Pw_forum at pwscf.org > http://www.democritos.it/mailman/listinfo/pw_forum > > > End of Pw_forum Digest, Vol 41, Issue 28 > -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] xspectra calculation
Dear Jiayu >And i think even for dipolar part, the direction of k vector should be >important in some cases, such as the SiO2 in the example. No, this is incorrect. The dipolar part cross section does not depend on k. >And if we >want to compare the results with some experiments, we should cut the >contribution of occupied states, that is, cut_occ_states = .true. >should be used. But we should shift the position by hand in order to >compare the results, cause i think it is very difficult to get the >accurate position in DFT, or even in atomic physics, it is a difficult >problem to determine the position of spectra. The "ef_r" should be the >fermi energy in scf calculation with core-hole, i think. On this second point you are right in the method but not on the reason why one should cut at somewhat lower values with respect to e_f. The problems that you can face are the following: 1) You have a system with a gap even in the presence of a core-hole . In this case if you cut exactly at the bottom of the conduction band (empty states) then the cut_occ_states procecure can miss this peak. So it is safer to cut at somewhat lower energy than the bottom of the conduction band. 2) You have a system without gap in the presence of a core-hole (either because it was a metal even without core-hole or because it was a small gap semiconductor that becomes a metal when the core-hole is inserted). In this case identification of where to cut is ill defined. In this case you should keep in mind that probably core hole effects are not correctly described. Of course, if DFT underestimates the gap you can easily end up in a metallic solution. All the best, M. Jiayu -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] xspectra calculation
>Dear Matteo, >So when we just do the dipolar part, we don't need to care about the >k vector, right? yes, it is not used. >Besides, in order to compare with an experimental spectrum, is it necessary >to cut >the occupied state below Fermi energy level within our Xspectra calculation ? >In that case, we should set "cut_occ_states" = .true. and >"ef_r" equal to the fermi energy we got in the scf calculation. Is it? Yes. However if you have a small gap insulator, introduction of a core-hole can lead to a metallic system (close the gap). In this case it is not clear where to cut. Actually in this case the static core-hole approximation is probably incorrect. For metals it is even worst. M. Best regards, Min Wu 2010-10 -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] xspectra calculation
Dear Min Wu, > >It seems i have found the problem. It's not the problem of the >xcoordcrys. I set it as .true. and the polarization vectors are (0,0,1) >and >(0,1,0). The xray k vector is the default value (1,0,0). >BTW, can we use the same vector for polarization and xay k moment? >e.g. Both of them are (1,0,0). Is it OK? Of course epsilon and k MUST be ortogonal otherwise what you are doing is meaningless. If you calculate the dipolar part only then the k-vector is not used and can take any value. > >The problem i found is that i set the "cut_occ_states" = .true. >Then it cut all the occupied state that i expected to see. >When i reset it to .false., i saw the expected peak. > Maybe your ef_r is not in the correct units... Of course you put the Fermi level in the presence of a core-hole, don't you ? >I have another problem, what does the "ef_r" do in the calculation? >For instance, i got fermi level of -5 eV with scf calculation. >The i set ef_r= -5/13.6 Ry. Then, in the calculated xspectra data, >where is >the Fermi level? It is ajusted to 0 eV, or still is the -5 eV? > zero, the energies are simply shifted. M. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] xspectra calculation (wumindt2)
dear Min Wu, the attachment do not go through the pw_forum, so I cannot do much about it. What I can tell you is that we calculate Co and LiCoO2 and we get a good agreement with experiments. Maybe you can try to compare with the following paper: Juhin et al. Phys. Rev. B 81, 115115 (2010) http://link.aps.org/doi/10.1103/PhysRevB.81.115115 Anyway, from four message what seems to be wrong (assuming the scf run to be correct) are the unit of the polarization vector (assuming you're dealing with the dipolar part only and assuming the peak you're referring to is dipolar). Did you set xcoordcrys to the proper value (see below)? For zhqt concerns CoO2, note that the pre-edge of CoO2 at the Co K-edge has a quadrupolar part, so if you stick to the dipolar calculation you want be able to reproduce the pre-edge peak. Note also that in the case of LiCoO2, which is probably not so different from yours, DFT fails in the pre-edge and you have to use DFT+U. In particular, remember that if you don't set the variable xcoordcrys=.false. your xepsilon and xkvec are in reduced coordinates. From Doc/INPUT_XSPECTRA xkvec(1:3)real(DP) DEFAULT=(1.0,0 .0,0.0) coordinates of the x-ray momentum k xepsilon(1:3) real(DP) DEFAULT=(1.0,0 .0,0.0) coordinates of the incident x-ray polarization vector xcoordcryslogical DEFAULT=.true. .true. to use crystal coordinates for k and epsilon Maybe you could try to reproduce our calculation on LiCoO2 so that you are sure of not having any errors with the input file. The paper is very detailed so you can compare every step in the calculation. All the best, M. >Message: 6 >Date: Mon, 18 Oct 2010 05:03:50 +0800 >From: "wumindt2" >Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >To: pw_forum at pwscf.org >Message-ID: >Content-Type: text/plain; charset="gb2312" >Dear Matteo, >I met some problem when calculating the XASs with the Xspectra. >I tested the example of quartz, and got the consistent result with the >published work. >Then i moved on to test another example of solid CO2, which has an >isotropic >symmetry according to C. Brouder's paper. But the X-ray absorption >spectrum >i got was totally wrong. The first sharp peak which is well-known >existing >in CO2 was not found. >We also tested a single CO2 molecule which is still a clear-cut >example. >The C atom and the two O atoms are all in the Z axis. So the >polarization vectors >of (0,0,1) and (1,0,0) are enough for this case. However, we still >cannot get the >right XAS. To make it easier for you to understand my problem, I >attached the input files of this calculation. >The GIPAW pseudopotentials i used were downloaded from the website of >QE. >Thanks a lot for the help. >Best regards, >Min Wu
[Pw_forum] Pw_forum Digest, Vol 40, Issue 19
Dear Min Wu, I think you should sit down a bit and try to solve this issue by yourself. This is not a problem concerning the code as you would have the same problem with any other code, but it concerns basic physics and group theory. In the future we plan to write a program to find the isotropic cross section with the sallest number of calculations possible from the knowledge of the symmetries of the lattice. However this is not yet done (I am not aware of any program doing this). So, as I always do in these case, you should si down,try to understand Ch. Bouder's paper and find the polarization vectors necessary to obtain the isotropic cross section. M. > > Message: 6 > Date: Tue, 12 Oct 2010 14:59:33 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Matteo, > > Thanks for the information, i read the C. Brouder the paper a little bit. > I'am still not sure how to choose the polarization vector. > For instance, we have a crystal with spacegroup of P42/MNM, point > group of 4/mmm. > According to the Table in C. Brouder's paper, this is a dichroism compound. > Thus, how can we choose the polarization vector when calculating the XAS > of this compound? > Can you please show me how? > > Thanks so much! > > Cheers, > > Min Wu > 2010-10-12 > > >> From: Matteo Calandra >> Reply-To: PWSCF Forum >> To: pw_forum at pwscf.org >> Subject: Re: [Pw_forum] Xspectra calculation (wumindt2) >> Date: Mon, 11 Oct 2010 10:08:16 +0200 >> >> Dear >> >> I assume you are talking of the dipolar part only. >> For the quadrupolar it is substantially more complicate. >> The number of independent calculations that you have >> to perform to obtain the isotropic cross section (powder) >> depends on the point group of the space group >> of your crystal. >> It is 1 for a cubic or tetraedric crystal, >> 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial >> (ot trichroic) crystal. >> I suggest you read >> C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 >> for more details. >> >> M. >> >> >>> >>> Message: 3 >>> Date: Sat, 09 Oct 2010 22:48:53 +0800 >>> From: "wumindt2" > >>> Subject: Re: [Pw_forum] Xspectra calculation >>> To: pw_forum at pwscf.org >>> Message-ID: > >>> Content-Type: text/plain; charset="gb2312" >>> >>> Dear matteo, >>> >>> Thanks. >>> >>> For dichroism compound, do we just need the in-plane and the c-axis >>> polarization vectors? >>> While for trichroism compound, do we need to calculate three different >>> polarization vectors? >>> Am i right? >>> >>> 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 > > > End of Pw_forum Digest, Vol 40, Issue 19 > > This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] Xspectra calculation (wumindt2)
Dear I assume you are talking of the dipolar part only. For the quadrupolar it is substantially more complicate. The number of independent calculations that you have to perform to obtain the isotropic cross section (powder) depends on the point group of the space group of your crystal. It is 1 for a cubic or tetraedric crystal, 2 for a uniaxial crystal and it is 3, 4, 6 for a biaxial (ot trichroic) crystal. I suggest you read C. Brouder J. Phys.: Condens. Matter 2 (1990) 701-738 for more details. M. > > Message: 3 > Date: Sat, 09 Oct 2010 22:48:53 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] Xspectra calculation > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear matteo, > > Thanks. > > For dichroism compound, do we just need the in-plane and the c-axis > polarization vectors? > While for trichroism compound, do we need to calculate three different > polarization vectors? > Am i right? > > Best regards, >
[Pw_forum] Xspectra calculation
Dear Wumindt2, the fact that different polarization directions can be equivalent or not in a solid depends only on the symmetry of your lattice (thus on the crystal structure) only. So the general response to your question is given by the theory of crystal symmetries. M. > -- > > Message: 1 > Date: Sat, 09 Oct 2010 11:11:16 +0800 > From: "wumindt2" > Subject: [Pw_forum] Xspectra calculation > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear Xspectra users, > > I met a problem when calculating the X-ray absorption spectra with > the Xspectra code. > Concern about the polarization, ?// is the polarization along the c > axis, while ?? is the polariztion > in the plane. It's easy to define the ?// , since normally (0,0,1) > is the direction of c axis. > But for ?? polarization, what does "in plane" mean? Are any > directions in the a,b plane > will cause the same result? For instance, will (1,0,0) ,(0,1,0) or > (1,1,0) polarization direction > have the same spectra? > > Thank you very much for any help. > > Cheers, > > Min Wu > 2010-10-8 > -- next part -- > An HTML attachment was scrubbed... > URL: > http://www.democritos.it/pipermail/pw_forum/attachments/20101009/5fd9f157/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 40, Issue 16 > > This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] problem with Xspectra
Dear Min Wu, usually the mistake you did (using the 1s wavefunction with the core-hole instead of that without the core-hole) leads to small differences in the case of K-edge, as the two wavefunction are probably very similar. This is not true for L1 edges (that you can calculate with the current program) or generally speaking, less deep edges (L,M and so on). However, even in the case of K-edges it can be important. So I suggest you repeat the last step of your calculation (the XSPECTRA one) using the core wfc without a core-hole as this is the correct thing to do. All the best, M. > > Message: 1 > Date: Wed, 06 Oct 2010 02:53:07 +0800 > From: "wumindt2" > Subject: Re: [Pw_forum] problem with Xspectra > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Dear matteo, > > Thank you very much! > I've got the picture now. > > BTW, in my previous calculation, i mistakenly extract the core wavefunction > from the pseudopotential WITH a core hole. But the result seems good > when compared > with the experiment. Does it happen often? > > Cheers, > > Min Wu > 2010-10-5 > > > >> From: matteo calandra >> Reply-To: PWSCF Forum >> To: pw_forum at pwscf.org >> Subject: Re:[Pw_forum] problem with Xspectra >> Date: Tue, 5 Oct 2010 10:49:48 +0200 >> >> Dear Min Wu, >> >> the pseudopotentials to be used for the absorbing atom >> in Xspectra are those having >> the label _gipaw, two examples are: >> >> Fe.pbe-sp-mt_gipaw.UPF >> Fe.star1s-pbe-sp-mt_gipaw.UPF >> >> The first one has no core-hole and has full gipaw informations >> while the second one has core-hole and full gipaw informations. >> Gipaw informations mean many things. What you need to know is that >> GIPAW informations include the presence of the >> all-electron wavefunction for the 1s core state. >> >> Now when you run a simulation you first need to calculate the charge >> density in the presence of a core-hole and thus use pseudo >> Fe.star1s-pbe-sp-mt_gipaw.UPF . This is done by a standard pw.x >> scf calculation using this pseudo. >> In a second step you need to calcuate the Xanes cross >> section and this is done by the Xspectra code. >> >> In the calculation of the matrix element appearing in the >> Xanes cross-section (Fermi golden rule) the initial 1s state >> IN THE ABSENCE of a core hole is needed. This information is contanined >> in the pseudo potential WITHOUT the core hole (Fe.pbe-sp-mt_gipaw.UPF). >> Thus you simply extract this wavefunction using the script given with the >> Xspectra disribution and you put the name of the file produced by the script >> in the input file of the Xspectra program. >> >> You cannot use the 1s core function with the core hole simply >> because this is >> wrong as the matrix element inthe cross section involves the product >> between the initial and final states and the initial state has no core hole. >> >> M. >>> Message: 1 >>> Date: Tue, 05 Oct 2010 00:42:50 +0800 >>> From: "wumindt2" > >>> Subject: [Pw_forum] problem with Xspectra >>> To: pw_forum at pwscf.org >>> Message-ID: > >>> Content-Type: text/plain; charset="gb2312" >>> >>> Hi, >>> >>> I'm a new user of Xspectra. >>> >>> In the Xspectra example given in the pwscf code, it calculates the >>> XAS using the pseudopotential >>> without core hole level. In this case, we need to extract the core >>> wavefunction from the GIPAW >>> pseudopotential when we run the xspectra.x. >>> >>> Now there are pseudopotentials with core hole, normally named as >>> *.star1s*.UPF. So here is >>> my question, after the SCF calculation, do we still need to extract >>> the core wavefunction from the >>> peusopotential of the absorbing atom? >>> >>> If the answer is yes, then why we choose the core wavefunction from >>> the pseudopotential as the ground >>> state, rather than the core wavefunction after the SCF calculation? >>> >>> Thanks! >>> >>> Min Wu >>> 2010-10-4 >> >> >> >> This message was sent using IMP, the Internet Messaging Program. >> >> >> ___ >> Pw_forum mailing list >> Pw_forum at pwscf.org >> http://www.democritos.it/mailman/listinfo/pw_forum >> > This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] problem with Xspectra
Dear Min Wu, the pseudopotentials to be used for the absorbing atom in Xspectra are those having the label _gipaw, two examples are: Fe.pbe-sp-mt_gipaw.UPF Fe.star1s-pbe-sp-mt_gipaw.UPF The first one has no core-hole and has full gipaw informations while the second one has core-hole and full gipaw informations. Gipaw informations mean many things. What you need to know is that GIPAW informations include the presence of the all-electron wavefunction for the 1s core state. Now when you run a simulation you first need to calculate the charge density in the presence of a core-hole and thus use pseudo Fe.star1s-pbe-sp-mt_gipaw.UPF . This is done by a standard pw.x scf calculation using this pseudo. In a second step you need to calcuate the Xanes cross section and this is done by the Xspectra code. In the calculation of the matrix element appearing in the Xanes cross-section (Fermi golden rule) the initial 1s state IN THE ABSENCE of a core hole is needed. This information is contanined in the pseudo potential WITHOUT the core hole (Fe.pbe-sp-mt_gipaw.UPF). Thus you simply extract this wavefunction using the script given with the Xspectra disribution and you put the name of the file produced by the script in the input file of the Xspectra program. You cannot use the 1s core function with the core hole simply because this is wrong as the matrix element inthe cross section involves the product between the initial and final states and the initial state has no core hole. M. > Message: 1 > Date: Tue, 05 Oct 2010 00:42:50 +0800 > From: "wumindt2" > Subject: [Pw_forum] problem with Xspectra > To: pw_forum at pwscf.org > Message-ID: > Content-Type: text/plain; charset="gb2312" > > Hi, > > I'm a new user of Xspectra. > > In the Xspectra example given in the pwscf code, it calculates the > XAS using the pseudopotential > without core hole level. In this case, we need to extract the core > wavefunction from the GIPAW > pseudopotential when we run the xspectra.x. > > Now there are pseudopotentials with core hole, normally named as > *.star1s*.UPF. So here is > my question, after the SCF calculation, do we still need to extract > the core wavefunction from the > peusopotential of the absorbing atom? > > If the answer is yes, then why we choose the core wavefunction from > the pseudopotential as the ground > state, rather than the core wavefunction after the SCF calculation? > > Thanks! > > Min Wu > 2010-10-4 This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] negative values in XANES (jiayudai)
Dear Jiayu, I assume you're using XSPECTRA to calculate Xanes K-edge. Maybe you can better specify what does it means "negative absorption". If this means that the value on the XANES intensity is negative then you must have some problem somewhere as the cross section implemented in XSPECTRA is positive definite. However, from your e-mail it is not very clear if the absorption is positive definite (as you say) or if the energy scale (the x axis in the plot) is negative but not the X-ray absorption intensity (y-axis in the plot). If y is positive and x is negative, then you simply forgot to specify the variable ef_r in the XSPECTRA input file. This variable tells you the zero energy of the scale. From the XSPECTRA input file: ef_r real(DP)DEFAULT=0.0 Fermi energy in Rydberg. This value combined with the option cut_occupied_states can be used to exclude the occupied states in a smooth way from the final plot. I hope it helps, M. > Dear developers and users, > > I am doing the calculation for the XANES of CHx system. There is a > problem that the absorption is always negative, locating at about > -100 eV. According to my >understanding, the absorption should be > positive. Besides, the fermi energy in >my systems is very high, > about tens of eV (high pressure). Therefore, if i used the cutoff of > fermi energy, the absorption should be very small. Is it > >reasonable? Or there is some problems in the calculations? > > Thanks in advance. > > Jiayu This message was sent using IMP, the Internet Messaging Program.
[Pw_forum] Additional informations about XSpectra - Peaks, at negative energies?
Dear Christian, indeed it is related to the cut_occ_states option. If this option is false you also see the occupied states at negative energies. This is very useful in many case. If now you want to cut the occupied states, simply rerun xspectra using the cut_occ_states=.true. option and the spectrum will be smoothly cut out at the e_f you have specified. Note also that you don't need to perform again the full lanczos process but only to replot the curve, namely use the option xonly_plot=.true., in the namelist _xspectra provided you have kept the .sav file with all the informations on the previously performed lanczos process, namely the a and b coefficients. If you give a look at the diamond example in the examples/XSpectra_examples of the distribution then you will find all the informations you need. Finally, if the cut_occ_states option takes too much time then there are other parameters to tune that can drastically reduce the time needed. To understand how cut_occ_states works you can look at Phys. Rev. B 54, 7334?7349 (1996) sections III A and III b. However I suggest you do not touch the parameters related to cut_occ_states unless you know what you do. All the best, M. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] Additional informations about XSpectra
Dear Christian, here the answers to your questions: > (1) is the energy range (xemin,xemax) referred to the Fermi energy > of the preliminar scf calculation? No, it is referred to the Fermi level given in input in the xspectra file (input variable ef_r in the input_xspectra namelist. This means that if you do not specify the Fermi level then ef_r=0.0 and they are referred to the energy zero of the preliminary scf run. > (1) is there a special convention for the components of the wavevector > and of the polarization vector? The defaults are (1,0,0) and (0,1,0); > shouldn't they be orthogonal? This depends on the variable xcoordcrys. If the variable xcoordcrys=.true. then xkvec and xepsilon are the crystalline components of the wavevector and the polarization vector with respect to the direct lattice vectors as chosen by QE. On the contrary, if xcoordcrys=.false. then they are the components with respect to the cartesian axes (in direct space). Note that also the xkvec components are in direct space as this is customary in the XAS community. xkvec and xepsilon should of course be orthogonal. If they are not, then the code gives you a warning in output but it does not stop. The reason is that if you do a dipolar calculation only, then xkvec is irrelevant. > (3) last line of input, after the $cut_occ section > (question already posted on past 2/7 in this forum) it is the number of k-point necessary to calculate the XANES cross section. In practice you can chose to calculate the charge density with a given number of k-points and then the XANES with a larger one. Generally the convergence of the xanes cross section with respect to k-points is slower thant that of the charge density. This is similar to what you do with a density of states calculation, namely you first calculate the charge density with Nk k points and then the dos with a much larger Nk' grid. All the best, M. M. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] Ni.pbe-sp-mt_gipaw.UPF: one pseudopotential for two, oxidation states? (Merlin Meheut)
Dear Merlin, the pseudopotential Ni.pbe-sp-mt_gipaw.UPF includes 3s and 3p semicore states as Paolo giannozzi suggested and it is a norm conseving pseudopotential. As far as I remember it was also tested on bulk Ni and the agreement with the experimental pressure was fine. Of course, being a Norm conseving with semicore states, it will require a cutoff of at least of 150 Ryd and not of 27.0 Ryd as your input file seems to suggest. M. >> ibrav=2, celldm(1) =6.65, nat= 1, ntyp= 1, >> nspin=2, >> starting_magnetization(1)=0.5, >> degauss=0.02, >> smearing='mp', >> occupations='smearing', >> ecutwfc =27.0 >> ecutrho =300.0 >> / -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] x-ray spectra with "Fermi-Dirac" electronic smearing., (Huolin Xin)
>Dear developers, >Since when did quantum espresso start to offer XANEFS calculations? I >remember I sent an email on this forum half of a hear ago to ask >whether anyone is interested in developing an EELS calculation plugin. >I got no response. Dear Huolin Xin, I think it is roughly 1 year that the XSpectra package is included in the CVS version and maybe somewhat less (I don't quite remember) that it is included in the official distribution. However, you should be careful with EELS. XSpectra calculates K-edge XAS (both dipolar and quadrupolar terms). EELS is similar to XAS but not identical. In particular the angular dependence of EELS spectra is not purely dipolar but there is a monopole term (that usually is assumed negligible even when it is not). So using the XAS dipolar simulations to interpret EELS spectra must be done "cum grano salis". We have planned to include EELS calculation in XSpectra, however we have not yet started. M. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] x-ray spectra with "Fermi-Dirac" electronic (Jayu)
Dear Jiayu, if I understand correctly you would like to calculate K-edge XAS at high temperature including the contribution of Fermi functions in the Fermi golden rule. If this is what you would like to do, this is currently not implemented in XSPECTRA, as we always assume the temperature to be negligible with respect to the energy of the electronic excitations (1 eV=11605 Kelvin). In practice we assume that the XAS spectra is temperature independent, or, better, the only temperature dependence comes from the thermal expansion of the crystal structure. This is generally true except when vibrations contribute to the XAS spectra. Increasing temperature increase atomic vibrations and it is known in some case to wakly affect the spectra in the pre-edge region. However even in this case I guess that the problem can be solved without the need of introducing Fermi functions in the XAS cross section. You will find more details on the XAS equation implemented in Christos Gougoussis, Matteo Calandra, Ari P. Seitsonen, and Francesco Mauri, Phys. Rev. B 80, 075102 (2009) http://link.aps.org/doi/10.1103/PhysRevB.80.075102 Equation 1. What the fermi_level option in XSPECTRA does is simply calculating the Fermi level with a given electronic smearing. The electronic smearing is used in the case of metals to improve the sampling of the Fermi surface when a finite grid of k-points is used. In the case of a metallic system, as your case is, then XSPECTRA does not calculate the Fermi level and stops as this quantity can be simply read from the pw.x scf output that you must have run before XSPECTRA. Finally, note that to calculate the electronic structure and the cross section, any smearing available in pw.x should also work on XSPECTRA. However this is not equivalent in adding Fermi functions to the Fermi golden rule. Matteo -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
[Pw_forum] upf2plotcore.sh new version (Jiayu-Day)
Dear Jiayu-Day I have just committed a new version of the upf2plotcore.sh script that extracts core-wavefunctions from upf version 1 and upf version 2. Thanks to Ari Seitsonen providing the script. Matteo. -- * * * * Matteo Calandra, Charge de Recherche (CR1) Institut de Min?ralogie et de Physique des Milieux Condens?s de Paris Universit? Pierre et Marie Curie, tour 16, case 115 4 Place Jussieu, 75252 Paris Cedex 05 France Tel: +33-1-44 27 52 16 Fax: +33-1-44 27 37 85 http://www.impmc.jussieu.fr/~calandra
