<div><div dir="auto">Dear Dr Fabien Tran,</div><div dir="auto"><br></div><div dir="auto">Thank you very much for your very clear explanation. Then all my confusions have been cleared.</div></div><div dir="auto"><br></div><div dir="auto">Ding</div><div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, 4 May 2020 at 11:24 pm, Tran, Fabien <<a href="mailto:fabien.tran@tuwien.ac.at">fabien.tran@tuwien.ac.at</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<p>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.<br>
</p>
<p><br>
</p>
<p><br>
</p>
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<div id="m_4278824141166684793divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> Wien <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>> on behalf of Ding Peng <<a href="mailto:ding.peng@monash.edu" target="_blank">ding.peng@monash.edu</a>><br>
<b>Sent:</b> Monday, May 4, 2020 2:46 PM</font></div></div></div><div dir="ltr" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif"><div style="word-wrap:break-word;line-break:after-white-space"><div id="m_4278824141166684793divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><br>
<b>To:</b> A Mailing list for WIEN2k users<br>
<b>Subject:</b> Re: [Wien] Questions about difference electron density map</font>
<div> </div>
</div>
<div>Dear Dr Fabien Tran,
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>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? </div>
<div><br>
</div>
<div>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)?</div>
<div><br>
</div>
<div>Many thanks and sorry for asking so many questions, which may seem to be silly.</div>
<div><br>
</div>
<div>Ding</div>
<div><br>
<blockquote type="cite">
<div>On 4 May 2020, at 7:26 pm, Tran, Fabien <<a href="mailto:fabien.tran@tuwien.ac.at" target="_blank">fabien.tran@tuwien.ac.at</a>> wrote:</div>
<br>
<div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
Hi,<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
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:<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
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 <span style="font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;background-color:rgb(255,255,255)">difference </span>because
the spikes of the two densities should cancel such that the difference can be integrated easily.<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
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.<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
<br>
</div>
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<hr style="display:inline-block;width:929.03125px">
<div id="m_4278824141166684793divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span> </span>Wien <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>>
on behalf of Ding Peng <<a href="mailto:ding.peng@monash.edu" target="_blank">ding.peng@monash.edu</a>><br>
<b>Sent:</b><span> </span>Monday, May 4, 2020 12:45 PM<br>
<b>To:</b><span> </span>A Mailing list for WIEN2k users<br>
<b>Subject:</b><span> </span>Re: [Wien] Questions about difference electron density map</font>
<div> </div>
</div>
<div>Dear Dr Fabien Tran,
<div><br>
</div>
<div>I had tried your suggestions and it indeed has worked. The difference charge density map looks reasonable. Many thanks for that!</div>
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>Many thanks,</div>
<div>Ding</div>
<div><br>
</div>
<div><br>
<div><br>
<blockquote type="cite">
<div>On 3 May 2020, at 2:50 am, Tran, Fabien <<a href="mailto:fabien.tran@tuwien.ac.at" target="_blank">fabien.tran@tuwien.ac.at</a>> wrote:</div>
<br>
<div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
If I'm not wrong (I have never tried this combination of keywords), you can do that by specifying<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
DIFF ADD<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
at the 6th line of case.in5(c). See Sec. 8.14.3 of the user's guide for explanation.<br>
</div>
<div style="margin-top:0px;margin-bottom:0px;font-family:Calibri,Arial,Helvetica,sans-serif;font-size:16px;font-style:normal;font-weight:normal;letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;background-color:rgb(255,255,255);text-decoration:none">
<br>
</div>
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<div id="m_4278824141166684793divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt"><b>From:</b><span> </span>Wien <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>>
on behalf of Ding Peng <<a href="mailto:ding.peng@monash.edu" target="_blank">ding.peng@monash.edu</a>><br>
<b>Sent:</b><span> </span>Saturday, May 2, 2020 6:41 PM<br>
<b>To:</b><span> </span>A Mailing list for WIEN2k users<br>
<b>Subject:</b><span> </span>Re: [Wien] Questions about difference electron density map</font>
<div> </div>
</div>
<div>
<div>
<div dir="auto">Dear Dr Fabien Tran,</div>
</div>
<div dir="auto"><br>
</div>
<div dir="auto">Thanks for your reply. Very clear explanation as it is always.</div>
<div dir="auto"><br>
</div>
<div dir="auto">I got another question about the difference charge density calculation.<br>
</div>
<div dir="auto">For magnetic materials (including ferromagnetic, anti ferromagnetic or quadrupolar-antiferromagntic materials etc.), what I can think of to calculate the difference charge density is </div>
<div dir="auto"><br>
</div>
<div dir="auto">1) calculate the valence charge density (option “rho”) for spin-up electrons (x lapw5 -up)</div>
<div dir="auto"><br>
</div>
<div dir="auto">2) calculate the valence charge density (Option “rho” for spin-down electrons (x lapw5 -dn)</div>
<div dir="auto"><br>
</div>
<div dir="auto">3) sum 1 and 2 and subtract them by the superposed atomic valence densities (option “Over”.</div>
<div dir="auto"><br>
</div>
<div dir="auto"><br>
</div>
<div dir="auto">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 ?</div>
<div dir="auto"><br>
</div>
<div dir="auto">Many thanks,</div>
<div dir="auto">Ding</div>
<div><br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sun, 3 May 2020 at 12:16 am, Tran, Fabien <<a href="mailto:fabien.tran@tuwien.ac.at" target="_blank">fabien.tran@tuwien.ac.at</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-style:solid;border-left-color:rgb(204,204,204);padding-left:1ex">
As I already said in my previous email, the last column is the occupancy.<br>
An occupancy of zero means that the corresponding band is not included<br>
in the valence electron density (stored case.clmval, that is used for plotting).<br>
"Energy to separate semicore and valence states" seems to be a prediction<br>
of what it means.<br>
<br>
<br>
From: Wien <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>> on behalf of Ding Peng <<a href="mailto:ding.peng@monash.edu" target="_blank">ding.peng@monash.edu</a>><br>
Sent: Saturday, May 2, 2020 5:23 PM<br>
To: A Mailing list for WIEN2k users<br>
Subject: Re: [Wien] Questions about difference electron density map<br>
<span> </span><br>
Dear Dr Fabien Tran,<br>
<br>
<br>
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?<br>
<br>
<br>
Sorry for asking so many questions in this email.<br>
<br>
<br>
Best regards,<br>
Ding<br>
<br>
<br>
<br>
On 2 May 2020, at 10:12 pm, Tran, Fabien <<a href="mailto:fabien.tran@tuwien.ac.at" target="_blank">fabien.tran@tuwien.ac.at</a>> wrote:<br>
<br>
<br>
<br>
>From your output2, we can see that you discarded the states that are below -0.3 Ry<br>
<br>
<br>
<br>
(the occupancy in the last column is zero for them) to calculate the electron density.<br>
You have to check that the number of remaining electrons used to calculate the<br>
valence electron density is the same as the number of electrons obtained from lstart to<br>
create the valence electron density from superimposed atomic densities.<br>
<br>
<br>
<br>
From: Wien <<a href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at" target="_blank">wien-bounces@zeus.theochem.tuwien.ac.at</a>> on behalf of Ding Peng <<a href="mailto:ding.peng@monash.edu" target="_blank">ding.peng@monash.edu</a>><br>
Sent: Saturday, May 2, 2020 1:11 PM<br>
To: A Mailing list for WIEN2k users<br>
Subject: Re: [Wien] Questions about difference electron density map<br>
<span> </span><br>
<br>
<br>
<br>
<br>
Dear Prof Peter Blaha and other WIEN2k experts,<br>
<br>
<span> </span><br>
<br>
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:<br>
<br>
<br>
<br>
<br>
<br>
By following your advices, I've checked the band ranges in output2 and they are :<span> </span><br>
<br>
<span> </span><br>
<br>
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? <span> </span><br>
<br>
<br>
Many thanks,<br>
Ding _______________________________________________<br>
</blockquote>
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</blockquote>
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</blockquote>
</div>
<br>
</div>
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</blockquote></div></div>