<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Dear Prof Laurence,<div class=""><br class=""></div><div class="">You say that Wien2k does not attempt to do any of the charged cell corrections that are in the literature, so besides the alignment of the electrostatic potential (or aligning the core states, as you suggested) are there other correction terms that must be taken into account?</div><div class=""><br class=""></div><div class="">I’m trying to simulate a p-type dopant, so I calculated a neutral supercell with the dopant (DOS shows an impurity band inside the band gap which is missing an electron to be full), calculated a charged supercell by adding an extra electron (DOS shows the impurity band is full) and calculated the same supercell for the pure bulk material.</div><div class="">To calculate the formation energy of the charged state, I tried to align the core states of an atom far from the dopant comparing the values from the charged supercell and from the bulk material, but I observed that variations in the same order of magnitude are are also present in the core states of the same atom in the neutral supercell (comparing to bulk). Since the core states in the neutral supercell should be identical to the bulk, does this mean that the variations I see in the charged supercell might be numerical variations?</div><div class=""><br class=""></div><div class="">Also, I did the structural optimizations using the PBE functional but after that I used the modified Becke-Johnson potential (mBJ) to get a better band gap and DOS.</div><div class="">Calculating the formation energy of the charged state using the PBE functional gives me a positive formation energy but it gives me a negative formation energy when using the mBJ.</div><div class="">Since I depend not only on the total energy of each supercell to do the calculation but also on the value of the Fermi energy of the bulk material, are any of these values not correctly estimated using the mBJ and therefore I should use the values obtained using the PBE?</div><div class=""><br class=""></div><div class="">Finally, regarding the PRL paper by Pantelides, if I understood correctly, their method depends for instance on removing electrons from lower bands and adding them to higher bands. However, such a procedure is not possible in a Wien2k calculation, or is it?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Marcelo</div><div class=""><br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 12 Apr 2019, at 20:02, Laurence Marks <<a href="mailto:L-marks@northwestern.edu" class="">L-marks@northwestern.edu</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family: verdana, sans-serif;">What you are trying to do is generate an estimate of the energy dV*Q where dV is the potential offset, and Q is your charge. The atoms by the charged defect will not be close to the same as the bulk, you want one which is far enough away that it is a viable reference state. You then compare this to your reference material, which does not have to be a supercell and could be just bulk. (Sometimes it is easier to ensure that k-points and other things are identical by using a supercell without the defect.)</div><div class="gmail_default" style="font-family: verdana, sans-serif;"><br class=""></div><div class="gmail_default" style="font-family: verdana, sans-serif;">Be aware that Wien2k does not attempt to do any of the charged cell corrections that are in the literature. For these you are on your own! In principle you want to extrapolate with a series of cells of increasing size in order to calculate the defect-defect coupling energy as a function of cell size. And/or calculate the correction. I remember many years ago looking at this with Peter, and I am not sure either of us was terrible convinced by the corrections in the literature.</div><div class="gmail_default" style="font-family: verdana, sans-serif;"><br class=""></div><div class="gmail_default" style="font-family: verdana, sans-serif;">Also, be aware that the approach of charged cells assumes that there is no interaction between, for instance, holes and the defect. I recently did a (neutral) calculation of a Ni vacancy in NiO. What I expected to find was two Ni3+, but instead I found a couple of delocalized hole on O sites near the vacancy. (I still need to ponder whether I believe this.) A charged cell calculation where one adds two electrons at the same time as one creates a Ni vacancy will not include the electrostatic interaction between the (negative) vacancy and the delocalized hole.</div><div class="gmail_default" style="font-family: verdana, sans-serif;"><br class=""></div><div class="gmail_default" style="font-family: verdana, sans-serif;">Also, there is a recent paper by Pantelides in PRL (with some later comments by others) where he disagrees with the conventional approach. I do not know who is right.</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Apr 12, 2019 at 12:34 PM Marcelo Barbosa <<a href="mailto:marcelo.b.barbosa@gmail.com" class="">marcelo.b.barbosa@gmail.com</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="overflow-wrap: break-word;" class="">
Dear Prof Laurence,
<div class=""><br class="">
</div>
<div class="">First of all, thank you for stepping into the discussion and for clarifying the difference between a pseudo-potential calculation and an all-electron code in this situation.</div>
<div class=""><br class="">
</div>
<div class="">Can I then use the core energies obtained using for example "grep :1S case.scf”?</div>
<div class=""><br class="">
</div>
<div class="">By the way, I have another question…</div>
<div class="">This correction is only needed for a charged cell and, as far as I understood, for the method performed in the case of pseudo-potential calculations the alignment must be done between the charged supercell and a supercell of the same size from
the bulk material.</div>
<div class="">However, for the procedure you described, the core energy difference should be calculated between the charged supercell and the same supercell in the non-charged state, correct?</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Marcelo</div>
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 11 Apr 2019, at 19:19, Laurence Marks <<a href="mailto:L-marks@northwestern.edu" target="_blank" class="">L-marks@northwestern.edu</a>> wrote:</div>
<br class="gmail-m_3972884625836882224Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="gmail_default" style="font-family:verdana,sans-serif">I think this conversation has gone in an incorrect direction. What you are trying to do is align the relative energies/potential as there is an offset due to subtraction of the mean inner
potential (to avoid singularities) that is different for charged and non-charged cells.</div>
<div class="gmail_default" style="font-family:verdana,sans-serif"><br class="">
</div>
<div class="gmail_default" style="font-family:verdana,sans-serif">With a pseudo-potential calculation, the electrostatic potential is readily available so people use it to align.</div>
<div class="gmail_default" style="font-family:verdana,sans-serif"><br class="">
</div>
<div class="gmail_default" style="font-family:verdana,sans-serif">With an all-electron code the electrostatic potential can be generated, but there are far easier methods to align! All you need to do is compare the core energies of atoms well away from the
defect. This gives you the relevant energy axis shift.</div>
<div class="gmail_default" style="font-family:verdana,sans-serif"><br class="">
</div>
<div class="gmail_default" style="font-family:verdana,sans-serif">Then you have to make whatever correction you trust....which is not a trivial issue.</div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Apr 11, 2019 at 11:34 AM Marcelo Barbosa <<a href="mailto:marcelo.b.barbosa@gmail.com" target="_blank" class="">marcelo.b.barbosa@gmail.com</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Thank you very much for your help!
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Marcelo<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 11 Apr 2019, at 16:16, SM Alay-e-Abbas <<a href="mailto:alayabbas@gmail.com" target="_blank" class="">alayabbas@gmail.com</a>> wrote:</div>
<br class="gmail-m_3972884625836882224gmail-m_5655902535517498212Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">
<div class="">--> Since I need to calculate the electrostatic potential, is following method the correct approach? Is it also correct for spin polarized calculations?</div>
<div class=""><i class="">For electrostatic potentials you should be using case.vcoul. I don't think that the magnetic order matters here since there is only one output for electrostatic potential (*.vcoul). </i></div>
<div class=""><br class="">
</div>
<div class="">--> Create the case.in5 file with the correct plane and number of points to be calculated</div>
<div class=""><i class="">and s</i><i class="">et ny = 1!</i></div>
<div class=""><i class=""><br class="">
</i></div>
<div class="">--> Use “x lapw5 -d” to create the file lapw5.def and then change the unit 9 from “case.clmval” to “case.vtotal”<br class="">
</div>
<div class=""><i class="">for electrostatic potentials, it should be case.vcoul</i>. </div>
<div class=""><br class="">
</div>
<div class="">--> Run lapw5 and get the values in case.rho</div>
<i class="">The results you should be looking for are in case.rho_onedim</i><br class="">
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Apr 11, 2019 at 12:09 PM Marcelo Barbosa <<a href="mailto:marcelo.b.barbosa@gmail.com" target="_blank" class="">marcelo.b.barbosa@gmail.com</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div class="">Dear Alay,
<div class=""><br class="">
</div>
<div class="">Thank you very much for your help!</div>
<div class=""><br class="">
</div>
<div class="">I am able to use your method to select the appropriate plane and the number of points in that plane to be calculated using lapw5.</div>
<div class="">I just not entirely sure that I correctly understood the rest of the procedure by reading the user’s guide.</div>
<div class=""><br class="">
</div>
<div class="">Since I need to calculate the electrostatic potential, is following method the correct approach? Is it also correct for spin polarized calculations?</div>
<div class=""><br class="">
</div>
<div class="">- Create the case.in5 file with the correct plane and number of points to be calculated</div>
<div class="">- Set “iuntits” to ATU in case.in5 to get the values in Ry</div>
<div class="">- Set “cnorm” to VAL in case.in5</div>
<div class="">- Use “x lapw5 -d” to create the file lapw5.def and then change the unit 9 from “case.clmval” to “case.vtotal”</div>
<div class="">- Run lapw5 and get the values in case.rho</div>
<div class=""><br class="">
</div>
<div class="">Best regards,</div>
<div class="">Marcelo</div>
<div class=""><br class="">
<div class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 4 Apr 2019, at 21:30, SM Alay-e-Abbas <<a href="mailto:alayabbas@gmail.com" target="_blank" class="">alayabbas@gmail.com</a>> wrote:</div>
<br class="gmail-m_3972884625836882224gmail-m_5655902535517498212gmail-m_-2220089208851169109Apple-interchange-newline">
<div class="">
<div dir="ltr" class="">Hello Marcelo,
<div class=""><br class="">
</div>
<div class="">You may do this by selecting an appropriate atom centered plane (with reasonable width) and then setting npy = 1 in case.in5 before running lapw5. See section 8.13.3 of the userguide for more details.</div>
<div class=""><br class="">
</div>
<div class="">Best Regards,</div>
<div class=""><br class="">
</div>
<div class="">Alay </div>
</div>
<br class="">
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Apr 4, 2019 at 5:40 PM Marcelo Barbosa <<a href="mailto:marcelo.b.barbosa@gmail.com" target="_blank" class="">marcelo.b.barbosa@gmail.com</a>> wrote:<br class="">
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear Sirs,<br class="">
<br class="">
When comparing the formation energies of two charge states of an impurity in a semiconductor as a function of the Fermi level, it is said that a correction term must be added to align the electrostatic potential from the supercell with the impurity (using a
position far from the impurity) and from a supercell of the pure bulk material with the same size (see e.g. DOI: 10.1063/1.1682673).<br class="">
<br class="">
The electrostatic potential is calculated in LAPW0, but how can I find the value corresponding to a specific position in my supercell?<br class="">
<br class="">
<br class="">
Best regards,<br class="">
Marcelo<br class="">
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<div dir="ltr" class=""><span style="font-size:12.8px" class="">Professor Laurence Marks</span><br class="">
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