<div dir="ltr"><div>Dear all,</div><div><br></div><div>I have a question about using polyhedral constraints. </div><div><br></div><div>I collected neutron PDF data of an amorphous hydrocarbon sample (no obvious peak above 15-20A in G(r)), which is believed to be linked polyaromatichydrocarbon. I hope to fit it starting from the model of Benzopyrene or anthracene, etc (or even a mixture of them). Does anyone know how to make a restraint to keep the molecule (Benzopyrene or anthracene) rigid?</div>
<div><br></div><div>Thank you very much!</div><div>Kuo</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Fri, Dec 6, 2013 at 10:40 AM, <span dir="ltr"><<a href="mailto:matt.tucker@stfc.ac.uk" target="_blank">matt.tucker@stfc.ac.uk</a>></span> wrote:<br>
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<p class="MsoNormal"><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)">Dear Christopher,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><u></u><span style="color:rgb(31,73,125)"><span>1)<span style="font:7pt/normal "Times New Roman";font-size-adjust:none;font-stretch:normal">
</span></span></span><u></u><span style="color:rgb(31,73,125)">Can RMCProfile fit x-ray PDF?: Yes<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><span style="color:rgb(31,73,125)">What Chris Kerr says is not strictly true. RMCProfile can fit x-ray PDF data.
<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><span style="color:rgb(31,73,125)">The x-ray F(Q) can be fitted with the XRAY_RECIPROCAL_DATA keyword. However, the x-ray form factors have to be in the data file and it has to be convolved with the simulation box size. There is a program
call xray_to_rmc that will do this for you if supplied the data in the usual rmc format.<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><span style="color:rgb(31,73,125)">For the x-ray PDF, since the q-dependant part has been divided out you can treat this as a neutron PDF with different weights. These weightings are defined using the keyword NEUTRON_COEFFICIENTS (sorry
a bit confusing I know).<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><span style="color:rgb(31,73,125)">We are writing a tutorial example to show how all this works and it will be in the minor update 6.5.2. This will be out in the next few weeks.<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><span style="color:rgb(31,73,125)">As Chris Kerr says there are plans to fit the x-ray PDF in a more rigorous way. Once this is implemented it will be useful for all x-ray PDF data, as it will make a fairer comparison regardless of the
atomic radii<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><u></u><span style="color:rgb(31,73,125)"><span>2)<span style="font:7pt/normal "Times New Roman";font-size-adjust:none;font-stretch:normal">
</span></span></span><u></u><span style="color:rgb(31,73,125)">How do you fit nanoparticles with RMCProfile?<u></u><u></u></span></p>
<p><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p><span style="color:rgb(31,73,125)">Sadly this is not an easy question to answer, there are three possible approaches.
<u></u><u></u></span></p>
<p style="margin-left:72pt">
<u></u><span style="color:rgb(31,73,125)"><span>a.<span style="font:7pt/normal "Times New Roman";font-size-adjust:none;font-stretch:normal">
</span></span></span><u></u><span style="color:rgb(31,73,125)">The first is to treat the data as a bulk sample if the particle is large. If not then a modification function for the particle size could be applied but this isn’t implemented at present.<u></u><u></u></span></p>
<p style="margin-left:72pt">
<u></u><span style="color:rgb(31,73,125)"><span>b.<span style="font:7pt/normal "Times New Roman";font-size-adjust:none;font-stretch:normal">
</span></span></span><u></u><span style="color:rgb(31,73,125)">The second (as Chris says) is to put one particle in a large box and only fit out to a distance where it does not see its periodic repeat (RMC uses periodic boundary conditions).
<u></u><u></u></span></p>
<p style="margin-left:72pt">
<u></u><span style="color:rgb(31,73,125)"><span>c.<span style="font:7pt/normal "Times New Roman";font-size-adjust:none;font-stretch:normal">
</span></span></span><u></u><span style="color:rgb(31,73,125)">Finally if you can build a starting configuration with particles in a matrix that is not too large (> ~40,000 atoms), then you can use the various constraints/restraints to hold things together and
model it as normal. This of course is not trivial but probably the ideal solution.
<u></u><u></u></span></p>
<p class="MsoNormal" style="margin-left:54pt"><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-left:54pt"><span style="color:rgb(31,73,125)">If you tell us some more about your system we can advise what your best approach is most likely to be.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)">Best wishes,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)">Matt<u></u><u></u></span></p>
<p class="MsoNormal"><span style="color:rgb(31,73,125)"><u></u> <u></u></span></p>
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<p class="MsoNormal"><span style="color:rgb(31,73,125)">. <u></u><u></u></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-family:"Tahoma","sans-serif";font-size:10pt">From:</span></b><span lang="EN-US" style="font-family:"Tahoma","sans-serif";font-size:10pt"> <a href="mailto:rmcprofile-users-bounces@rmcprofile.org" target="_blank">rmcprofile-users-bounces@rmcprofile.org</a> [mailto:<a href="mailto:rmcprofile-users-bounces@rmcprofile.org" target="_blank">rmcprofile-users-bounces@rmcprofile.org</a>]
<b>On Behalf Of </b>Christopher J. Wright<br>
<b>Sent:</b> 02 December 2013 00:36<br>
<b>To:</b> <a href="mailto:rmcprofile-users@rmcprofile.org" target="_blank">rmcprofile-users@rmcprofile.org</a><br>
<b>Subject:</b> [RMCProfile-users] X-ray PDF use<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal"><span lang="EN-US">Hi,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">I am working with PDF data collected from an x-ray synchrotron source. The samples are nanoparticles of various size and compositions. Is it possible to model these particles using RMCprofile?<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you very much,<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Christopher J. Wright<u></u><u></u></span></p>
<p class="MsoNormal"><span lang="EN-US">Brown University Chemistry Department<u></u><u></u></span></p>
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<br><p>--
<br>Scanned by iCritical.
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<br></blockquote></div><br><br clear="all"><br>-- <br><div>Kuo Li</div><div>Joint Insitute for Neutron Science</div><div>Oak Ridge National Laborotary</div><div>Carnegie Institution of Washington</div><div>Office:865-241-3114</div>
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