[Pw_forum] k-points for xLi2MnO3-(1-x)LiMO2
Seid Mohammed Geleto
smgbadb at gmail.com
Mon Apr 18 17:58:43 CEST 2016
Hi, I am in need of generating the k-points for xLi2MnO3-(1-x)LiMO2,
M=Mn,Ni,Co, etc. to calculate electronic and band. So how can I
generate this k-points for this materials?
Thank you very much!
Seid M. Geleto
PhD student
Jimma Institute of Technology
School of Materials Science and Engineering
Jimma, Ethiopia
On 4/18/16, pw_forum-request at pwscf.org <pw_forum-request at pwscf.org> wrote:
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> Today's Topics:
>
> 1. Re: PAW orthonormality and obtaining S|psi> (Henry J Seeley)
> 2. Re: Plotband.x (Manu Hegde)
> 3. Re: PAW orthonormality and obtaining S|psi> (Paolo Giannozzi)
> 4. Re: Plotband.x (Giovanni Cantele)
> 5. Re: Plotband.x (Francesco Pelizza)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 17 Apr 2016 18:15:12 -0700
> From: Henry J Seeley <hseeley at uoregon.edu>
> Subject: Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <780fcb6402c3eb91161c8a182b576acf at uoregon.edu>
> Content-Type: text/plain; charset=US-ASCII; format=flowed
>
> Thank you Natalie,
>
> I'll look into plotpaw, but I need to obtain the wavefunctions for
> specific states for my projections.
>
> -Hank Seeley
>
>
> On 2016/04/16 13:43, Holzwarth, Natalie wrote:
>> Dear Henry,
>> I don't know how to output the full PAW wavefunctions in
>> quantum espresso. Did you want to evaluate ithem on a grid of real
>> space points? There is a program called plotpaw.f90 that seems to
>> output the full PAW density on a grid of points in real space. Is
>> this close to what you want to do? In any case, I never used this
>> program and the top says "experimental and incomplete program ...".
>> Perhaps Paolo might clarify this? It could be that this existent
>> code could be modified for your purposes?? Hopefully someone else
>> might have a better answer.
>> Sincerely, Natalie
>>
>> N. A. W. Holzwarth email:
>> natalie at wfu.edu
>> Department of Physics web:
>> http://www.wfu.edu/~natalie
>> Wake Forest University phone:
>> 1-336-758-5510
>> Winston-Salem, NC 27109 USA office: Rm. 300 Olin
>> Physical Lab
>>
>> On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley <hseeley at uoregon.edu>
>> wrote:
>>
>>> Thank you Natalie,
>>>
>>> I've already used projwfc.x for these systems without the 'pawproj'
>>> option; I didn't realize I was doing this incorrectly! I'll
>>> definitely
>>> make this correction...
>>> I am still interested in obtaining the wavefunctions however. How do
>>> I
>>> go about getting the "correct" wavefunctions for the PAW method?
>>>
>>> Thank you again,
>>> Hank Seeley
>>>
>>> On 2016/04/16 07:21, Holzwarth, Natalie wrote:
>>>> Dear Henry,
>>>> In the PAW method, the atomic pseudo basis functions are not
>>>> designed to be orthogonal to each other, but there is a "dual
>>>> relationship" <p_i|\tilde{\psi}_j>=\delta_{ij} with the projector
>>>> function p_i. One can use the projector function to estimate the
>>>> charge associated with an atomic site within the augmentation
>>> sphere
>>>> about that site. (Some notes are enclosed about this in case you
>>> are
>>>> interested. The main equations are correct, but the programming
>>>> details are no longer true.) Paolo Giannozzi programmed this
>>> into
>>>> quantum espresso in version 5.3.0. Perhaps this might suite
>>> your
>>>> needs?? In order to use it you need to use &projwfc:
>>>>
>>>> &projwfc
>>>> pawproj= .true. , << new option
>>>> outdir='$outd/', << old options; change as appropriate
>>>> prefix='$label',
>>>> filpdos='pdos',
>>>> Emin=-25.0, Emax=25.0, DeltaE=0.01,
>>>> ngauss=0, degauss=0.01
>>>> /
>>>>
>>>> Sincerely, Natalie Holzwarth
>>>>
>>>> N. A. W. Holzwarth email:
>>>> natalie at wfu.edu
>>>> Department of Physics web:
>>>> http://www.wfu.edu/~natalie
>>>> Wake Forest University phone:
>>>> 1-336-758-5510
>>>> Winston-Salem, NC 27109 USA office: Rm. 300
>>> Olin
>>>> Physical Lab
>>>>
>>>> On Fri, Apr 15, 2016 at 8:02 PM, Henry J Seeley
>>> <hseeley at uoregon.edu>
>>>> wrote:
>>>>
>>>>> Hello all,
>>>>>
>>>>> I'm currently trying to use Quantum Espresso to generate the
>>>>> eigenfunctions for bulk and slab systems of PbS, which I then
>>> plan
>>>>> on projecting onto one another to determine the relative surface
>>> or
>>>>> bulk character of specific slab states. I've generated my sample
>>>>> systems and have run the scf/nscf calculations, but I've hit some
>>>>> trouble with the eigenvectors obtained from 'pw_export.x'. I have
>>> a
>>>>> couple questions that I hope some of you may be able to answer.
>>> Of
>>>>> course all my input files will be attached.
>>>>>
>>>>> To my surprise I found that different eigenstates of the same
>>> system
>>>>> are NOT orthonormal (<psi_i|psi_i> ~= 0.75, abs(<psi_i|psi_j>) ~=
>>>>> 0.15). I've done some searching and determined this may have to
>>> do
>>>>> with the PAW psuedo-potentials I am using. Is the PAW method the
>>>>> problem here?
>>>>>
>>>>> In trying to troubleshoot this, I found that eigenstate
>>>>> orthonormality may be obtained by including the 'uspp_spsi =
>>> .TRUE.'
>>>>> option in the 'pw_export.x' input file, which produces S|psi>,
>>> which
>>>>> is orthonormal by <psi_i|S|psi_j>. Is this correct? If so, how
>>> can I
>>>>> project the two different systems on one another (bulk/slab),
>>> i.e.
>>>>> which system's eigenvector gets the 'S'?
>>>>>
>>>>> Finally (and sorry for all the questions at once), I've tried
>>> using
>>>>> the 'uspp_spsi = .TRUE.' option for both the bulk and slab
>>> systems,
>>>>> but I receive an error message for the bulk (but not the slab!):
>>>>>
>>>>> *** glibc detected *** pw_export.x: malloc(): memory corruption:
>>>>> 0x0000000002b3a650 ***
>>>>>
>>>>> This occurs right as pw_export.x tries to produce the S|psi>
>>> files.
>>>>> I'm at a loss, and cannot proceed to troubleshoot this by myself
>>> any
>>>>> further. Does anyone have any insight into:
>>>>> (A) Whether I'm even taking the right approach, or (B) Why I
>>> could
>>>>> be getting this error for the bulk system but not the slab?
>>>>>
>>>>> Thank you all for your time,
>>>>> Hank Seeley
>>>>> University of Oregon, Chemistry Dept.
>>>>> _______________________________________________
>>>>> Pw_forum mailing list
>>>>> Pw_forum at pwscf.org
>>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>>
>>>>
>>>> _______________________________________________
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>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> ------------------------------
>
> Message: 2
> Date: Sun, 17 Apr 2016 23:34:30 -0400
> From: Manu Hegde <mhegde at uwaterloo.ca>
> Subject: Re: [Pw_forum] Plotband.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CA+g44DvfV5KdSwgaRD4BLkXDjK1HjYqDEXm8Bv44Q7otvr6ztA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Giovanni,
>
> Thanks for your advice.
>
> I have calculated band structure for the zinc blende GaP lattice. When I
> plotted using gnuplot it looks okay (plotgnu_gap.ps). But .ps format from
> the plotband.x (plotband_gap.ps) does not look properly and there some
> bands crossing. I am not sure why it is happening like this. I have
> attached both the files.
>
> Regards,
> Manu
>
> Dr.Manu Hegde
> Postdoctoral Fellow
> Department of Chemistry
> University of Waterloo
>
> Waterloo, ON, N2L 3G1
>
>
> On Wed, Apr 6, 2016 at 6:26 AM, Giovanni Cantele <
> giovanni.cantele at spin.cnr.it> wrote:
>
>> Quite likely, you did not calculate the band structure along a path in
>> the
>> Brillouin zone, but used the output of the scf calculation (k-point
>> grid).
>> After running pw.x with calculation=?scf? or calculation=?relax?,
>> you need to rerun it with a new input file, calculation=?bands? and
>> K_POINTS card containing a suitable path of k-points. See also examples
>> of
>> band structure calculation included in the QE-package.
>>
>> You can set Emin (Emax) to the value of the lowest (highest) eigenvalue),
>> unless you need to select some specific energy range.
>>
>> Giovanni
>>
>> PS Users of this forum are usually kindly requested to sign messages with
>> affiliation
>>
>> On 06 Apr 2016, at 05:25, Manu Hegde <mhegde at uwaterloo.ca> wrote:
>>
>> Hello All,
>>
>> I was trying to plot band structure of PbTiO3, I could only see dots in
>> bands.ps file. I am not sure what is the reason for this. Is it due to
>> the wrong k-point selection?. I am also not sure about energy selection
>> along y-axis (Emax, Emin). I have attached bands.ps file please have a
>> look. Please help to overcome from this problem.
>>
>> Thanks and Regards
>>
>> Manu
>> <pbtio.bands.ps>_______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>>
>> --
>>
>> Giovanni Cantele, PhD
>> CNR-SPIN
>> c/o Dipartimento di Fisica
>> Universita' di Napoli "Federico II"
>> Complesso Universitario M. S. Angelo - Ed. 6
>> Via Cintia, I-80126, Napoli, Italy
>> e-mail: giovanni.cantele at spin.cnr.it
>> Phone: +39 081 676910
>> Skype contact: giocan74
>>
>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>> Web page: http://people.na.infn.it/~cantele
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>>
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 18 Apr 2016 08:54:34 +0200
> From: Paolo Giannozzi <p.giannozzi at gmail.com>
> Subject: Re: [Pw_forum] PAW orthonormality and obtaining S|psi>
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID:
> <CAPMgbCutJOB5m5pPJBHc97hXNoqEvHUU=eA2Tn=Npk77zH+_BQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> On Sat, Apr 16, 2016 at 10:43 PM, Holzwarth, Natalie <natalie at wfu.edu>
> wrote:
>
> There is a program called plotpaw.f90 that seems to output the full PAW
>> density on a grid of points in real space. Is this close to what you
>> want to do? In any case, I never used this program and the top says
>> "experimental and incomplete program ...". Perhaps Paolo might clarify
>> this?
>>
>
> "experimental" because it is not thoroughly tested (but as far as I know it
> works), "incomplete" because it only computes the all-electron charge
> density on a line of points in real space. One might use code "pp.x" to
> plot the PAW charge density in 3D, but a very dense FFT grid is required to
> have a decent representation. Extending the codes to wavefunctions
> shouldn't be difficult but not straightforward either.
>
> On Sat, Apr 16, 2016 at 12:39 PM, Henry J Seeley <hseeley at uoregon.edu>
> wrote:
>
> I've already used projwfc.x for these systems without the 'pawproj'
>> option; I didn't realize I was doing this incorrectly!
>
>
> I do not think it is incorrect (or at least, I hope it isn't), it is just a
> different way to project
>
> Paolo
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>
> ------------------------------
>
> Message: 4
> Date: Mon, 18 Apr 2016 09:56:10 +0200
> From: Giovanni Cantele <giovanni.cantele at spin.cnr.it>
> Subject: Re: [Pw_forum] Plotband.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <FF1DE29F-249D-486A-8972-42697D3224A3 at spin.cnr.it>
> Content-Type: text/plain; charset="utf-8"
>
> bands crossing are spurious and they are due to the fact that, after running
> bands.x (or in the case you have not used it at all), the bands order might
> be incorrect. That means that the n-th band (that is, the band that at each
> k-point is
> plotted as n-th eigenvalue) might actually contain, at different k-points,
> energies belonging to different bands. In this case, if you not only plot
> the points but also connect them with lines, you might see spurious
> connection lines between
> different bands. The way to cure this problem is to run bands.x before
> plotband.x, but with a sufficient number of k-points (if they are too
> distant bands.x might fail in following a band, that is, in assigning a
> given eigenvalue to a band).
>
> Giovanni
>
>
>
>> On 18 Apr 2016, at 05:34, Manu Hegde <mhegde at uwaterloo.ca> wrote:
>>
>> Hi Giovanni,
>>
>> Thanks for your advice.
>>
>> I have calculated band structure for the zinc blende GaP lattice. When I
>> plotted using gnuplot it looks okay (plotgnu_gap.ps
>> <http://plotgnu_gap.ps/>). But .ps format from the plotband.x
>> (plotband_gap.ps <http://plotband_gap.ps/>) does not look properly and
>> there some bands crossing. I am not sure why it is happening like this. I
>> have attached both the files.
>>
>> Regards,
>> Manu
>>
>> Dr.Manu Hegde
>> Postdoctoral Fellow
>> Department of Chemistry
>> University of Waterloo
>>
>> Waterloo, ON, N2L 3G1
>>
>>
>> On Wed, Apr 6, 2016 at 6:26 AM, Giovanni Cantele
>> <giovanni.cantele at spin.cnr.it <mailto:giovanni.cantele at spin.cnr.it>>
>> wrote:
>> Quite likely, you did not calculate the band structure along a path in the
>> Brillouin zone, but used the output of the scf calculation (k-point grid).
>> After running pw.x with calculation=?scf? or calculation=?relax?,
>> you need to rerun it with a new input file, calculation=?bands? and
>> K_POINTS card containing a suitable path of k-points. See also examples of
>> band structure calculation included in the QE-package.
>>
>> You can set Emin (Emax) to the value of the lowest (highest) eigenvalue),
>> unless you need to select some specific energy range.
>>
>> Giovanni
>>
>> PS Users of this forum are usually kindly requested to sign messages with
>> affiliation
>>
>>> On 06 Apr 2016, at 05:25, Manu Hegde <mhegde at uwaterloo.ca
>>> <mailto:mhegde at uwaterloo.ca>> wrote:
>>>
>>> Hello All,
>>>
>>> I was trying to plot band structure of PbTiO3, I could only see dots in
>>> bands.ps <http://bands.ps/> file. I am not sure what is the reason for
>>> this. Is it due to the wrong k-point selection?. I am also not sure about
>>> energy selection along y-axis (Emax, Emin). I have attached bands.ps
>>> <http://bands.ps/> file please have a look. Please help to overcome from
>>> this problem.
>>>
>>> Thanks and Regards
>>>
>>> Manu
>>> <pbtio.bands.ps
>>> <http://pbtio.bands.ps/>>_______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>> <http://pwscf.org/mailman/listinfo/pw_forum>
>> --
>>
>> Giovanni Cantele, PhD
>> CNR-SPIN
>> c/o Dipartimento di Fisica
>> Universita' di Napoli "Federico II"
>> Complesso Universitario M. S. Angelo - Ed. 6
>> Via Cintia, I-80126, Napoli, Italy
>> e-mail: giovanni.cantele at spin.cnr.it
>> <mailto:giovanni.cantele at spin.cnr.it>
>> Phone: +39 081 676910 <tel:%2B39%20081%20676910>
>> Skype contact: giocan74
>>
>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>> <http://www.researcherid.com/rid/A-1951-2009>
>> Web page: http://people.na.infn.it/~cantele
>> <http://people.na.infn.it/~cantele>
>>
>>
>> _______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>> http://pwscf.org/mailman/listinfo/pw_forum
>> <http://pwscf.org/mailman/listinfo/pw_forum>
>>
>> <plotband_gap.ps><plotgnu_gap.ps>_______________________________________________
>> Pw_forum mailing list
>> Pw_forum at pwscf.org
>> http://pwscf.org/mailman/listinfo/pw_forum
>
> --
>
> Giovanni Cantele, PhD
> CNR-SPIN
> c/o Dipartimento di Fisica
> Universita' di Napoli "Federico II"
> Complesso Universitario M. S. Angelo - Ed. 6
> Via Cintia, I-80126, Napoli, Italy
> e-mail: giovanni.cantele at spin.cnr.it
> Phone: +39 081 676910
> Skype contact: giocan74
>
> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
> Web page: http://people.na.infn.it/~cantele
>
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>
> ------------------------------
>
> Message: 5
> Date: Mon, 18 Apr 2016 09:15:31 +0100
> From: Francesco Pelizza <francesco.pelizza at strath.ac.uk>
> Subject: Re: [Pw_forum] Plotband.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <571497A3.8010103 at strath.ac.uk>
> Content-Type: text/plain; charset="windows-1252"
>
> Sorry to jump in this argument. I may be not of much help.
>
> For the question of overlapping bands or strange mixing of bands...In my
> experience, bands become easier to be plotted if when you run bands.x
> you add in the input file the flag: no_overlap= .true.
>
> That flag avoid eigenvalues overlapping and even plotband.x does a nice
> job.
>
> Francesco
> University of Strathclyde
>
>
>
> On 18/04/16 08:56, Giovanni Cantele wrote:
>> bands crossing are spurious and they are due to the fact that, after
>> running bands.x (or in the case you have not used it at all), the
>> bands order might be incorrect. That means that the n-th band (that
>> is, the band that at each k-point is
>> plotted as n-th eigenvalue) might actually contain, at different
>> k-points, energies belonging to different bands. In this case, if you
>> not only plot the points but also connect them with lines, you might
>> see spurious connection lines between
>> different bands. The way to cure this problem is to run bands.x before
>> plotband.x, but with a sufficient number of k-points (if they are too
>> distant bands.x might fail in following a band, that is, in assigning
>> a given eigenvalue to a band).
>>
>> Giovanni
>>
>>
>>
>>> On 18 Apr 2016, at 05:34, Manu Hegde <mhegde at uwaterloo.ca
>>> <mailto:mhegde at uwaterloo.ca>> wrote:
>>>
>>> Hi Giovanni,
>>>
>>> Thanks for your advice.
>>>
>>> I have calculated band structure for the zinc blende GaP lattice.
>>> When I plotted using gnuplot it looks okay (plotgnu_gap.ps
>>> <http://plotgnu_gap.ps/>). But .ps format from the plotband.x
>>> (plotband_gap.ps <http://plotband_gap.ps/>) does not look properly
>>> and there some bands crossing. I am not sure why it is happening like
>>> this. I have attached both the files.
>>>
>>> Regards,
>>> Manu
>>>
>>> Dr.Manu Hegde
>>> Postdoctoral Fellow
>>> Department of Chemistry
>>> University of Waterloo
>>>
>>> Waterloo, ON, N2L 3G1
>>>
>>>
>>> On Wed, Apr 6, 2016 at 6:26 AM, Giovanni Cantele
>>> <giovanni.cantele at spin.cnr.it <mailto:giovanni.cantele at spin.cnr.it>>
>>> wrote:
>>>
>>> Quite likely, you did not calculate the band structure along a
>>> path in the Brillouin zone, but used the output of the scf
>>> calculation (k-point grid). After running pw.x with
>>> calculation=?scf? or calculation=?relax?,
>>> you need to rerun it with a new input file, calculation=?bands?
>>> and K_POINTS card containing a suitable path of k-points. See
>>> also examples of band structure calculation included in the
>>> QE-package.
>>>
>>> You can set Emin (Emax) to the value of the lowest (highest)
>>> eigenvalue), unless you need to select some specific energy range.
>>>
>>> Giovanni
>>>
>>> PS Users of this forum are usually kindly requested to sign
>>> messages with affiliation
>>>
>>>> On 06 Apr 2016, at 05:25, Manu Hegde <mhegde at uwaterloo.ca
>>>> <mailto:mhegde at uwaterloo.ca>> wrote:
>>>>
>>>> Hello All,
>>>>
>>>> I was trying to plot band structure of PbTiO3, I could only see
>>>> dots in bands.ps <http://bands.ps/> file. I am not sure what is
>>>> the reason for this. Is it due to the wrong k-point selection?.
>>>> I am also not sure about energy selection along y-axis (Emax,
>>>> Emin). I have attached bands.ps <http://bands.ps/> file please
>>>> have a look. Please help to overcome from this problem.
>>>>
>>>> Thanks and Regards
>>>>
>>>> Manu
>>>> <pbtio.bands.ps
>>>>
>>>> <http://pbtio.bands.ps/>>_______________________________________________
>>>> Pw_forum mailing list
>>>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>> --
>>>
>>> Giovanni Cantele, PhD
>>> CNR-SPIN
>>> c/o Dipartimento di Fisica
>>> Universita' di Napoli "Federico II"
>>> Complesso Universitario M. S. Angelo - Ed. 6
>>> Via Cintia, I-80126, Napoli, Italy
>>> e-mail: giovanni.cantele at spin.cnr.it
>>> <mailto:giovanni.cantele at spin.cnr.it>
>>> Phone: +39 081 676910 <tel:%2B39%20081%20676910>
>>> Skype contact: giocan74
>>>
>>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>>> Web page: http://people.na.infn.it/~cantele
>>> <http://people.na.infn.it/%7Ecantele>
>>>
>>>
>>> _______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>>
>>>
>>> <plotband_gap.ps><plotgnu_gap.ps>_______________________________________________
>>> Pw_forum mailing list
>>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>> http://pwscf.org/mailman/listinfo/pw_forum
>>
>> --
>>
>> Giovanni Cantele, PhD
>> CNR-SPIN
>> c/o Dipartimento di Fisica
>> Universita' di Napoli "Federico II"
>> Complesso Universitario M. S. Angelo - Ed. 6
>> Via Cintia, I-80126, Napoli, Italy
>> e-mail: giovanni.cantele at spin.cnr.it
>> <mailto:giovanni.cantele at spin.cnr.it>
>> Phone: +39 081 676910
>> Skype contact: giocan74
>>
>> ResearcherID: http://www.researcherid.com/rid/A-1951-2009
>> Web page: http://people.na.infn.it/~cantele
>> <http://people.na.infn.it/%7Ecantele>
>>
>>
>>
>> _______________________________________________
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