[Wien] Questions about difference electron density map

[Ding Peng]

Dear Dr Fabien Tran,

Thank you very much for your very clear explanation. Then all my confusions
have been cleared.

Ding

On Mon, 4 May 2020 at 11:24 pm, Tran, Fabien <fabien.tran at tuwien.ac.at>
wrote:

> The way lstart works to generate case.sigma may be a bit confusing. The
> Ecut asked by lstart does not matter for case.sigma. Ecut is used to
> separate the core electrons from the others (semicore and valence) during
> the SCF calculation. In order to generate case.sigma with selected
> (semicore/valence) orbitals, you need to replace N by P in case.inst (not
> in case.inst_sigma) next to the selected orbitals and execute "x lstart"
> without -sigma. "x lstart -sigma" is used to generate case.sigma with all
> semicore/valence orbitals without having to replace all N by P in case.inst.
>
>
>
> ------------------------------
> *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Ding
> Peng <ding.peng at monash.edu>
> *Sent:* Monday, May 4, 2020 2:46 PM
>
> *To:* A Mailing list for WIEN2k users
> *Subject:* Re: [Wien] Questions about difference electron density map
>
> Dear Dr Fabien Tran,
>
> Thank you very much for your feedback. This is very helpful and solve my
> puzzle that confused me for a long time. I ask this question because I am
> not sure if my calculation on the difference charge density on CeB6 is
> correct.
>
> I'm still a bit confused about the superposed valence electron density. In
> the calculation of difference charge density, firstly I did "x lapw2" with
> Emin to separate the semi-core and valence state. Then I did x lstart
> -sigma. I'm not sure if the value of Ecut for this step should be the same
> as the one in the DFT initialisation step (i.e. set the Ecut to separate
> the core-state and the valence to avoid the core charge leaks out of
> MT-sphere). However, the valence electrons defined in the DFT
> initialisation step is not the same as the ones intrinsically defined by
> the chemists. For the case of CeB6, the valence electrons in chemistry are
> 4f, 5d and 6s electrons. This is different from the ones in the DFT
> initialisation step since we have to truncate 5s, 5p and sometimes 4d as
> well (i.e. treat them as the valence electrons) to avoid the charge leaks
> out of MT-sphere.
>
> So my question is: does this mean I should not use the "default valence
> states" module and have to turn to the "non-default valence states" module
> in the function of "electron density plots", and manually set 5s, 5p and 4d
> as core states to calculate the superposed atomic charge densities?
>
> If I follow this process, then I found an another problem, in the file
> lstart.def, the file case.inst replaced case.inst_sigma. But as Prof Peter
> Blaha had suggested (if my understanding of his words is correct), both
> case.inst and case.inst_sigma should be presented in lstart.def. Does that
> mean I should manually change included file names in lstart.def (add both
> "case.inst_sigma" and "case.inst" in it)?
>
> Many thanks and sorry for asking so many questions, which may seem to be
> silly.
>
> Ding
>
> On 4 May 2020, at 7:26 pm, Tran, Fabien <fabien.tran at tuwien.ac.at> wrote:
>
> Hi,
> Ideally, the integrated density difference should be zero, but due to
> numerical imprecision it won't be exactly the case. Since I don't know
> exactly what you want to do and the procedure you want to follow, it's
> difficult to give you more advice. Just be aware of two things:
> 1) Integrating accurately a quantity generated from lapw5 (uniform 3D
> grid) is difficult (or maybe impossible), because  the grid close to the
> nuclei (where the density is very spiky) needs to be extra dense.
> But, this should not be a problem for a density difference because the
> spikes of the two densities should cancel such that the difference can be
> integrated easily.
> 2) There is no particular problem at the edge of the cell. But, by
> integrating one should not count twice the same points: those which are on
> the opposite planes of the cell.
> ​
> ------------------------------
> *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Ding
> Peng <ding.peng at monash.edu>
> *Sent:* Monday, May 4, 2020 12:45 PM
> *To:* A Mailing list for WIEN2k users
> *Subject:* Re: [Wien] Questions about difference electron density map
>
> Dear Dr Fabien Tran,
>
> I had tried your suggestions and it indeed has worked. The difference
> charge density map looks reasonable. Many thanks for that!
>
> Can I ask you a question that if the net difference charge density in the
> unit cell (i.e. summation of the difference charge densities within the 3D
> unit cell) has to be zero? Because I know the errors introduced by the
> density samplings may be presented in LAPW5, especially at the edge of the
> unit cell. Also it can be affected by how many points are used to sample
> the grid-segment of the unit cell when using lapw5. I don't know if this
> sampling issue will affect the correctness of the charge density as well as
> the net difference charge density in the unit cell.
>
> Many thanks,
> Ding
>
>
>
> On 3 May 2020, at 2:50 am, Tran, Fabien <fabien.tran at tuwien.ac.at> wrote:
>
> If I'm not wrong (I have never tried this combination of keywords), you
> can do that by specifying
> DIFF ADD
> at the 6th line of case.in5(c). See Sec. 8.14.3 of the user's guide for
> explanation.​
>
> ------------------------------
> *From:* Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Ding
> Peng <ding.peng at monash.edu>
> *Sent:* Saturday, May 2, 2020 6:41 PM
> *To:* A Mailing list for WIEN2k users
> *Subject:* Re: [Wien] Questions about difference electron density map
>
> Dear Dr Fabien Tran,
>
> Thanks for your reply. Very clear explanation as it is always.
>
> I got another question about the difference charge density calculation.
> For magnetic materials (including ferromagnetic, anti ferromagnetic or
> quadrupolar-antiferromagntic materials etc.), what I can think of to
> calculate the difference charge density is
>
> 1) calculate the valence charge density (option “rho”) for spin-up
> electrons (x lapw5 -up)
>
> 2) calculate the valence charge density (Option “rho” for spin-down
> electrons (x lapw5 -dn)
>
> 3) sum 1 and 2 and subtract them by the superposed atomic valence
> densities (option “Over”.
>
>
> Can I ask if this is correct way to do the calculation of the difference
> charge density for magnetic materials? and also if there is an automatic
> option to directly calculate it in Wien2k “, just like option “Diff” for
> non-magnetic materials ?
>
> Many thanks,
> Ding
>
> On Sun, 3 May 2020 at 12:16 am, Tran, Fabien <fabien.tran at tuwien.ac.at>
> wrote:
>
>> As I already said in my previous email, the last column is the occupancy.
>> An occupancy of zero means that the corresponding band is not included
>> in the valence electron density (stored case.clmval, that is used for
>> plotting).
>> "Energy to separate semicore and valence states​" seems to be a prediction
>> of what it means.
>>
>>
>> From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at> on behalf of Ding
>> Peng <ding.peng at monash.edu>
>> Sent: Saturday, May 2, 2020 5:23 PM
>> To: A Mailing list for WIEN2k users
>> Subject: Re: [Wien] Questions about difference electron density map
>>
>> Dear Dr Fabien Tran,
>>
>>
>> Thanks for your reply. Actually, I set the Emin as -0.2 Ry, which means I
>> discarded the states that are below -0.2 Ry. Could I ask you if the last
>> number of the "band lines" is the occupancy?  If it is 0.0000000D+00
>> (double precision of 0), does  it mean that the corresponding band is
>> included as the valence state? Also I noticed there is a line "Energy to
>> separate semicore and valence states: -3.971792594507138E-002". Could  I
>> ask if the value "-3.971792594507138E-002" in this line the predicted Emin
>> by Wien2k?
>>
>>
>> Sorry for asking so many questions in this email.
>>
>>
>> Best regards,
>> Ding
>>
>>
>>
>> On 2 May 2020, at 10:12 pm, Tran, Fabien <fabien.tran at tuwien.ac.at>
>> wrote:
>>
>>
>>
>> From your output2, we can see that you discarded the states that are
>> below -0.3 Ry
>>
>>
>>
>> (the occupancy in the last column is zero for them) to calculate the
>> electron  density.
>> You have to check that the number of remaining electrons used to
>> calculate the
>> valence electron density is the same as the number of electrons obtained
>> from lstart to
>> create the valence electron density from superimposed ​atomic  densities.
>>
>>
>>
>> From: Wien <wien-bounces at zeus.theochem.tuwien.ac.at>  on behalf of Ding
>> Peng <ding.peng at monash.edu>
>> Sent: Saturday, May 2, 2020 1:11 PM
>> To: A Mailing list for WIEN2k users
>> Subject: Re: [Wien] Questions about difference electron density map
>>
>>
>>
>>
>>
>> Dear Prof Peter Blaha and other WIEN2k experts,
>>
>>
>>
>> Many thanks for your advice. Your explanation is very clear and I can
>> understand most of them. But I still get some questions to ask:
>>
>>
>>
>>
>>
>> By following your advices, I've checked the band ranges in output2 and
>> they are :
>>
>>  ​
>>
>>  Compared to the information in case.scf1, I was thinking the Emin should
>> be set slightly above  the energy band 10, which is from -0.3524 to -0.2916
>> (please correct me if I'm wrong). Does that mean the Emin of the whole
>> valence electrons should be set slightly above Emax of energy band 10,
>> which is -0.2916?
>>
>>
>> Many thanks,
>> Ding​            _______________________________________________
>>
>
>
> _______________________________________________
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
> SEARCH the MAILING-LIST at:
> http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20200504/50e88d71/attachment.html>