<div dir="ltr">What you have done is probably "right", although a 1x1x1 supercell is small and to do a formally correct calculation you would need to use a NxNxN supercell with N large and randomly occupy the positions but this would become very computationally expensive.<div><br></div><div>In a structure with partial occupancy, locally the atomic positions of your spinel will deviate from (x,x,x), similar to what you are finding. What XRD is measuring is a statistical average over the real local (x,y,z) which leads to an average (x,x,x). I expect that if you look carefully you will find that Shelx (or similar) is refining relatively large temperature factors for the oxygens which are being displaced. If you were to do the XRD at different temperatures you might find that the temperature factors are not going to small numbers as T-->0, rather to some large number due to the athermal disorder.</div><div><br></div><div>N.B., of course, you could also have a superstructure develop at lower temperatures and/or with more annealing of your sample.</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Mon, Sep 8, 2014 at 12:58 PM, shamik chakrabarti <span dir="ltr"><<a href="mailto:shamikphy@gmail.com" target="_blank">shamikphy@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div dir="ltr">Dear Laurence Marks Sir,
<div><br>
</div>
<div> Yes I have converted the 14 atomic Fd3m cell in 56 in equivalent atoms cell (generated from 1x1x1 supercell with target lattice primitive) to incorporate partial occupancy. However, before starting optimization I have checked
that implemented structure (used as input) provides the same XRD as the experimental structure with same relative intensities corresponding to different peaks. However that implemented structure shows a force as large as 200 mRy/bohr for some atoms and hence
can not be used for electronic structure calculation & we need optimization. Yes, it is true that as I have not kept the space group constraint to incorporate the partial occupancies the oxygen coordinate transformed from (x,x,x) to (x,y,z) during optimization,</div>
<div><br>
</div>
<div>But, then what should we do in this scenario?.....</div>
<div><br>
</div>
<div>Looking forward to your advice.</div>
<div><br>
</div>
<div>Thanks in advance.</div>
<div><br>
</div>
<div>with regards, </div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote"><div><div class="h5">On Mon, Sep 8, 2014 at 11:15 PM, Laurence Marks <span dir="ltr">
<<a href="mailto:L-marks@northwestern.edu" target="_blank">L-marks@northwestern.edu</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
<div dir="ltr">This is not a simple question to answer. In both DFT and XRD the symmetry of the structure is an input parameter, and in both cases it is sometimes wrong. The most obvious question to ask is whether you used the same Space Group for your refinement
in Wien2k that was used in the XRD refinement. I have a suspicion that you did not, as the presence of (x,x,x) positions implies a Space Group constraint and if you are getting (x,y,z) then you probably have a different symmetry in Wien2k.
<div><br>
<div>Check first that the symmetry is completely the same.</div>
<div><br>
</div>
<div>If they are the same, the question then would be why one gets (x,x,x) in the XRD refinement? It could be disorder or something else, but without more information it is hard to guess.</div>
<div><br>
</div>
</div>
</div>
<div class="gmail_extra">
<div>
<div><br>
<div class="gmail_quote">On Mon, Sep 8, 2014 at 11:37 AM, shamik chakrabarti <span dir="ltr">
<<a href="mailto:shamikphy@gmail.com" target="_blank">shamikphy@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div dir="ltr">Dear wien2k users,
<div><br>
</div>
<div> We have optimized atomic coordinates of a spinel cubic compound containing 56 atoms/cell. The most important variation we have seen between experimental structural coordinates & DFT (GGA+U) optimized coordinates is that.</div>
<div><br>
</div>
<div>the oxygen coordinate changes from (x,x,x) configuration to (x,y,z) configuration as we have not constrained the oxygen coordinates during optimization.</div>
<div><br>
</div>
<div>Although, this change has generated a structure having very small forces (< 1 mRy/Bohr) per atoms, the change in oxygen coordinates are significant (difference between x & z is 0.021) enough to change the relative intensities of different peaks of XRD
patterns. </div>
<div><br>
</div>
<div>Now my query is (before starting the experimental simulation by myself again!!) whether there is a way to constrain atomic coordinates such that it remain constrained to (x,x,x) configuration while changing the value of x?</div>
<div><br>
</div>
<div>& also whether such a constrained way should be adopted or should we accept the DFT optimized structure (a bit different from experimental one!!) as it is for further calculation?</div>
<div><br>
</div>
<div>Looking forward to your opinions & suggestions.</div>
<div><br>
</div>
<div>Thanks in advance,</div>
<div><br>
</div>
<div>with regards, <span><font color="#888888"><br clear="all">
<div> </div>
-- <br>
Shamik Chakrabarti<br>
Senior Research Fellow<br>
Dept. of Physics & Meteorology<br>
Material Processing & Solid State Ionics Lab<br>
IIT Kharagpur<br>
Kharagpur 721302<br>
INDIA </font></span></div>
</div>
</div>
</blockquote>
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<br>
<br clear="all">
<div><br>
</div>
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<span><font color="#888888">-- <br>
<div dir="ltr">Professor Laurence Marks<br>
Department of Materials Science and Engineering<br>
Northwestern University<br>
<a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a>
<div>Corrosion in 4D: <a href="http://MURI4D.numis.northwestern.edu" target="_blank">
MURI4D.numis.northwestern.edu</a><br>
Co-Editor, Acta Cryst A<br>
"Research is to see what everybody else has seen, and to think what nobody else has thought"<br>
Albert Szent-Gyorgi</div>
</div>
</font></span></div>
<br></div></div>
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<br clear="all">
<div><br>
</div>
-- <br>
Shamik Chakrabarti<br>
Senior Research Fellow<br>
Dept. of Physics & Meteorology<br>
Material Processing & Solid State Ionics Lab<br>
IIT Kharagpur<br>
Kharagpur 721302<br>
INDIA </span></div>
</div>
</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr">Professor Laurence Marks<br>Department of Materials Science and Engineering<br>Northwestern University<br><a href="http://www.numis.northwestern.edu" target="_blank">www.numis.northwestern.edu</a><div>Corrosion in 4D: <a href="http://MURI4D.numis.northwestern.edu" target="_blank">MURI4D.numis.northwestern.edu</a><br>Co-Editor, Acta Cryst A<br>"Research is to see what everybody else has seen, and to think what nobody else has thought"<br>Albert Szent-Gyorgi</div></div>
</div>