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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dear Mostafa,<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">We are about to release a minor update to the RMCProfile code and documentation which includes more detailed instructions on using X-ray data and some tips
on amorphous materials, too. Hopefully this will soon be of help to you. In the meantime, I will try to answer your questions.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-family:"Cambria","serif";color:black">1-</span><span style="color:black">
</span><span style="font-family:"Cambria","serif"">-The manual doesn’t mention how can create an
<b><u>initial configuration</u></b> of amorphous materials.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">This is actually quite a difficult problem. There are several approaches you could take. First you could simply place the right quantities of atoms into the configuration box at
random and allow the data to drive them to appropriate positions. Second, you could start from a crystal structure (if your material has a crystalline analogue) and run RMC with no data (and just minimum distance constraints, perhaps) to remove the long range
order. This can be problematic as it biases the result towards the crystal structure. Thirdly, you could use a model obtained from simulation such as molecular dynamics as your starting point.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-family:"Cambria","serif";color:black">2-</span><span style="color:black"> -</span><span style="font-family:"Cambria","serif"">The manual doesn’t mention how I can fit
<b><u>XRAY_REAL_SPACE_DATA</u></b>.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Currently we don’t have support for rigorous treatment of the X-ray real-space data. However, you can instead fit it by treating it as neutron data, changing the scattering length
in the calculations of the Faber-Ziman partials to Z (atomic number) and normalising to 1. This is a useful approximation and should be used with care (and always in addition to fitting the X-ray reciprocal space data).</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-family:"Cambria","serif";color:black">3-</span><span style="color:black">
</span><span style="font-family:"Cambria","serif"">- Is the program calculated the x-ray
<b><u>partial structure coefficients</u></b> like for neutron.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">For X-ray reciprocal space data you need to do some pre-processing. You will need to use a program called xray_to_rmc to take your F(Q) datafile and put it into the correct format
for RMC. This program also requires the .cfg file to obtain the concentrations of atoms and a file with the extension .xray which contains the form factor information as found in the International Tables. I’ve attached an example of this file, as its format
is extremely important. If you make your own then you must follow the spacing between numbers and decimal places exactly. The forthcoming release includes an updated version of this program which will be much easier to use.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">For X-ray real space data that you are treating as neutron, you will need to include a NEUTRON_COEFFICIENTS :: line in your .dat file with the coefficients calculated by using Z
as scattering length (and normalised to 1). If you don’t do this, the program only knows how to calculate the numbers for neutrons so the scaling will be completely wrong.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-family:"Cambria","serif";color:black">4-</span><span style="color:black">
</span><span style="font-family:"Cambria","serif"">-I use <b><u>PDFgetx3</u> </b>
for calculating F(q) and G(r),are these data need to rescaled and convolved.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I think that the F(Q) should be fine, but the definition of G(r) differs between PDFGetX3 and RMCProfile. You will need to use the function RMC is expecting. There is a useful paper
by Dave Keen which discusses this: <a href="http://journals.iucr.org/j/issues/2001/02/00/issconts.html">
http://journals.iucr.org/j/issues/2001/02/00/issconts.html</a> </span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-family:"Cambria","serif";color:black">5-</span><span style="color:black">
</span><span style="font-family:"Cambria","serif"">-When I use <b><u>rmc326</u></b> for converting the old *.<b><u>dat</u></b> file to
<b><u>version 6</u></b> it give me error that “<span style="color:red">'rmc326' is not recognized as a operable program or batch file.”<o:p></o:p></span></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I apologise – rmc326 should have been removed from the manual as it does not work. The good news is it is not so hard to make a new format .dat file by hand – there are examples
in the manual, but please let me know if you need help.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-family:"Cambria","serif";color:black">6-</span><span style="color:black">
</span><span style="font-family:"Cambria","serif";color:black">-how can I get atomeye file from rmc configuration file(cfg) in general because in the tutorial you use
<b><u>get_atomeye_sf6 and it if for this example only.</u></b></span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If you have a ‘classic’ format .cfg file just use the command rmc_to_atomeye which will ask for the information it needs. If you have a new style .rmc6f file
you will need to convert it to .cfg first, which is what the .bat file in the tutorial (get_atomeye_sf6) is doing – it should be easy enough to adapt this to suit your needs.<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>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I hope this is helpful, and as I said a new version which should make all this much clearer is imminent. We will let the mailing list know as soon as it’s online.<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 regards,<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"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> rmcprofile-users [mailto:rmcprofile-users-bounces@rmcprofile.org]
<b>On Behalf Of </b>Mostafa Saad<br>
<b>Sent:</b> 07 July 2014 09:37<br>
<b>To:</b> rmcprofile-users@rmcprofile.org<br>
<b>Subject:</b> [RMCProfile-users] Using RMCProfile For X-ray Data of Amorphous Materials<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:14.0pt;font-family:"Cambria","serif"">Dear all,</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<span style="font-size:14.0pt;font-family:"Cambria","serif"">I am working on amorphous materials and I have do high energy X-ray diffraction (Qmax=25 Ang) to my samples, now I try to use RMCProfile to model the structure of my samples.</span><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<o:p> </o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;text-align:justify">
<u><span style="font-size:14.0pt;font-family:"Cambria","serif"">First</span></u><span style="font-size:14.0pt;font-family:"Cambria","serif""> I follow the manual and tutorial but I face some problems like:</span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">1-</span><span style="font-size:7.0pt;color:black">
</span><span style="font-size:14.0pt;font-family:"Cambria","serif"">-The manual doesn’t mention how can create an
<b><u>initial configuration</u></b> of amorphous materials.</span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">2-</span><span style="font-size:7.0pt;color:black"> -</span><span style="font-size:14.0pt;font-family:"Cambria","serif"">The manual doesn’t mention how
I can fit <b><u>XRAY_REAL_SPACE_DATA</u></b>.</span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">3-</span><span style="font-size:7.0pt;color:black">
</span><span style="font-size:14.0pt;font-family:"Cambria","serif"">- Is the program calculated the x-ray
<b><u>partial structure coefficients</u></b> like for neutron.</span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">4-</span><span style="font-size:7.0pt;color:black">
</span><span style="font-size:14.0pt;font-family:"Cambria","serif"">-I use <b><u>PDFgetx3</u>
</b>for calculating F(q) and G(r),are these data need to rescaled and convolved.</span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">5-</span><span style="font-size:7.0pt;color:black">
</span><span style="font-size:14.0pt;font-family:"Cambria","serif"">-When I use <b>
<u>rmc326</u></b> for converting the old *.<b><u>dat</u></b> file to <b><u>version 6</u></b> it give me error that “<span style="color:red">'rmc326' is not recognized as a operable program or batch file.”</span></span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">6-</span><span style="font-size:7.0pt;color:black">
</span><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">-how can I get atomeye file from rmc configuration file(cfg) in general because in the tutorial you use
<b><u>get_atomeye_sf6 and it if for this example only.</u></b></span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:red"> </span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">Thank you in advance</span><o:p></o:p></p>
<p style="text-align:justify"><span style="font-size:14.0pt;font-family:"Cambria","serif";color:black">mostafa saad</span><o:p></o:p></p>
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