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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Benoit,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks for your email. Here is some more information about using RMCProfile with X-ray data. I am working on an example to show how it works for the next release
of the program (coming soon!) which will hopefully clear things up further.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">To fit an X-ray F(Q) you can use the XRAY_RECIPROCAL_SPACE_DATA keyword. The datafile that you use must contain the X-ray form factors and the data itself must
be convolved with the box size. There is a program called xray_to_rmc included with RMCProfile that will take data in the ‘normal’ rmc format, which is a two column ascii starting with the number of data points, like so:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">1200<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">#title line<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">x1 y1<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">x2 y2<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">. .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">. .<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">xn yn<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">and make a correctly formatted X-ray data file.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Currently an X-ray PDF can be treated like a neutron PDF but with different weightings. This is obviously an approximation and it’s important to fit the F(Q)
and Bragg (if applicable) as well. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">So for an X-ray PDF you use the NEUTRON_REAL_SPACE_DATA keyword, and supply a subordinate keyword NEUTRON_COEFFICIENTS which defines the weightings. These you
calculate in the same way as for neutrons but replace the scattering length, b, with atomic number of the element in question.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I hope this answers your query but please do get in touch if not or if you have further questions.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best wishes,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Helen<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:windowtext"> rmcprofile-users [mailto:rmcprofile-users-bounces@rmcprofile.org]
<b>On Behalf Of </b>Benoit Baptiste<br>
<b>Sent:</b> 05 May 2014 08:52<br>
<b>To:</b> rmcprofile-users@rmcprofile.org<br>
<b>Subject:</b> Re: [RMCProfile-users] RMCPROFILE<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">Dear Helen,<br>
<br>
I'm also working with x-ray PDFs (obtained with pdfgetx3 from Ag source measurements) and I've read there is maybe a way to use it in rmc profile. If it's possible, could you please give me more details about that ? I didn't find anything in the manual...<br>
<br>
Thanks in advance,<br>
<br>
Benoît Baptiste<br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Institut de Minéralogie, de Physique des Matériaux et de Cosmochimie<o:p></o:p></pre>
<pre>Plateforme de diffraction des rayons X<o:p></o:p></pre>
<pre>4 Place Jussieu - case courrier 115<o:p></o:p></pre>
<pre>75005 Paris <o:p></o:p></pre>
<p class="MsoNormal"><br>
<br>
Le 28/04/2014 13:22, <a href="mailto:helen.playford@stfc.ac.uk">helen.playford@stfc.ac.uk</a> a écrit :<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear H.Wu,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thank you for your email.
</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The keyword XRAY_RECIPROCAL_SPACE_DATA should work (but requires the data to be in a very specific format, which we are working on an example for), but at the
present time the keyword XRAY_REAL_SPACE_DATA is not implemented as there are questions over the accuracy of the Fourier transform. There are ways around this if you need to work with X-ray PDFs, which I can explain in more detail if necessary. Keywords with
X_ at the start are not implemented.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I am a little confused by your second paragraph. Do you have data from SiO2? In SiO2 each Si is coordinated to four, not five O atoms. The neighbour list file
you show is telling you that some atoms do not have the expected number of neighbours. If you were trying to run with the SiO2 polyhedral restraint this would have caused the errors. How did you generate the second file? It would not have produced errors as
each Si atom has 4 neighbours, but it’s important that the connectivity is correct (i.e. that Si atom #1 is really connected to O atoms #65, 74, 79 and 85).</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Please let me know if you would like further help working with X-ray data, or if you have any other questions.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Best wishes,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Helen</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-language:ZH-CN">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";mso-fareast-language:ZH-CN"> rmcprofile-users
[<a href="mailto:rmcprofile-users-bounces@rmcprofile.org">mailto:rmcprofile-users-bounces@rmcprofile.org</a>]
<b>On Behalf Of </b>????<br>
<b>Sent:</b> 22 April 2014 08:07<br>
<b>To:</b> rmcprofile-users<br>
<b>Subject:</b> [RMCProfile-users] RMCPROFILE</span><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">Dear author ,<o:p></o:p></p>
</div>
<div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> I 'm working with local atomic arrangement in disorder materials. When I study the RMCProfile software, I have some questions so need your help.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> In the SF6 example, I can get better results after studying the manual. But for the rmcsf6.dat file, I have some questions on the keyword of "NEUTRON_REAL(or RECIPROCAL)_SPACE_DATA". If I have X-ray diffraction data, I will modify
"NEUTRON" to "XRAY", but there will be some errors; but if I modify "NEUTRON" to "X", then it will success, but there is no important "rmcsf6_PDF1.csv" and "rmcsf6_SQ1.csv" files in the makefiles<span style="font-size:13.5pt;font-family:"Arial","sans-serif";color:#333333">.</span> I
don't know the reason. <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> Another question is restraint files. In the SF6 example, a S atom is adjacent with six O atoms and a O atom is adjacent with one S atom, because SF6 is unlinked octahedral material. When I research SiO2, SiO2 is linked tetrahedral
material, so there exists boundary problem. In principle, a Si atom is adjacent with five O atoms and a O atom is adjacent with two Si atom. But when I use neighbour_list.exe to create restraint files, SiO2.sio is:<o:p></o:p></p>
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<p class="MsoNormal"> 64<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">But there is error when I run the RMCProfile. I artificially change SiO2.sio file to SF6-like restraint files, there is no error. I don't know the reasons.This is modified file:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I know my expression have some questions, so I'm very sorry and hope you forgive me. Thank you very much!<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best wish!<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">H.Wu<o:p></o:p></p>
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<p>-- <br>
Scanned by iCritical. <o:p></o:p></p>
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<pre>_______________________________________________<o:p></o:p></pre>
<pre>rmcprofile-users mailing list<o:p></o:p></pre>
<pre><a href="mailto:rmcprofile-users@rmcprofile.org">rmcprofile-users@rmcprofile.org</a><o:p></o:p></pre>
<pre><a href="http://lists.rmcprofile.org/mailman/listinfo/rmcprofile-users">http://lists.rmcprofile.org/mailman/listinfo/rmcprofile-users</a><o:p></o:p></pre>
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