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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear H.Wu,<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">Thank you for your email.
<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">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.<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 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).<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">Please let me know if you would like further help working with X-ray data, or if you have any other 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"><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
[mailto:rmcprofile-users-bounces@rmcprofile.org] <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<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Dear author ,<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 '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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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>
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<p class="MsoNormal"><o:p> </o:p></p>
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<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"><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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