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Hi Helen,</p>
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Thanks for the help, and sorry for my delay.</p>
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So I've been playing with <span>StoG using your advice and had some success getting the tool to output the appropriately transformed G(r). Unfortunately it appears to suffer from large oscillations at low r that are not apparent in the GetX extracted PDFs.
At higher r, the two outputs match well, with the expected differences in tendency to limiting values at high-r.</span><span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,"Segoe UI","Segoe WP",Tahoma,Arial,sans-serif,serif,EmojiFont; font-size:13.3333px"><span></span></span></p>
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<span>I've been able however to get RMCProfile to fit the PDFgetX "G(r)" directly as it seems to be equivalent to the RMCProfile "D(R)," with a constant scale factor difference.</span></p>
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<span>My question is now: is it possible to get RMCprofile to do a local minimization of a scale factor? For example in Diffev, I can tell the program to quickly find the best scale factor after each RMC move. Finding a constant scale factor is linear and analytic,
I believe.</span></p>
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<span>Thanks again!</span></p>
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<span>Rob</span></p>
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<p><span style="color:rgb(33,33,33); font-size:13.3333px">Robert J. Koch, PhD</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<font color="#212121"><span style="font-size:13.3333px">Post-Doctoral Research Scientist</span></font><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Alfred University</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">New York State College of Ceramics</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span style="color:rgb(33,33,33); font-size:13.3333px">Inamori School of Engineering</span><br style="color:rgb(33,33,33); font-size:13.3333px">
<span tabindex="0" class="x_contextualExtensionHighlight x_ms-font-color-themePrimary x_ms-border-color-themePrimary x_ident_388_441" style="font-size:13.3333px">Alfred, NY 14802</span><br>
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<div id="x_divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" color="#000000" style="font-size:11pt"><b>From:</b> rmcprofile-users <rmcprofile-users-bounces@rmcprofile.org> on behalf of helen.playford@stfc.ac.uk <helen.playford@stfc.ac.uk><br>
<b>Sent:</b> Tuesday, August 15, 2017 11:01:00 AM<br>
<b>To:</b> rmcprofile-users@rmcprofile.org<br>
<b>Subject:</b> Re: [RMCProfile-users] Help with stog.exe or stog_new.exe</font>
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<div class="PlainText">Hi Rob,<br>
<br>
You're quite right about the D(r) vs G(r) terminology. It's also important to remember that the Q-space function output by the PDFget programs has usually (I believe) been multiplied by Q, so in order for the process of converting it to an RMCProfile-compatible
dataset to be successful it needs to be in a form which has not been multiplied by Q.<br>
<br>
A crash at that point when running StoG usually means it is unhappy about the choice of histogram binning - sometimes this can be a little unpredictable, but usually if the bin size is 0.02 Å and the first point is, say, 0.01, it works. I'll summarise below
the questions stog_new will ask you and my advice on answering them.<br>
<br>
Number of files to include - this is a throwback to a previous incarnation of the program, and should be 1<br>
File name - should be in two-column ascii format with the first line containing the number of points and the second being a title or comment<br>
Q min and max - as it sounds<br>
y-offset and scale - y-offset is a constant that is added to the data, as StoG expects an S(Q) which goes from ~0 at low-Q to 1 at high Q, and y-scale is a scaling factor to account for differences in normalisation/problems
with the data (should hopefully be very close to 1) <br>
x-offset - this should be half the histogram bin width<br>
Output file names - your choice of file name. I always include the _stog suffix to ensure that I know what they are in the future!<br>
Maximum r - your choice, e.g. 40<br>
Number of r points - ideally the number that gets you an r-spacing of 0.02, e.g. 2000<br>
Window function y/n? - whether or not you want to use the Lorch function (should usually be no)<br>
Number density - must match whatever simulation box you are going to use, e.g. the crystallographic density<br>
Add values - can enter a small number here which will be added to the Q-space data to try and get it closer to 0 at the point at which you truncate it for the FT. I do not usually use this, and answer this
question with a 0<br>
Try again - can try a different small offset by entering it here, or just say no to move on<br>
Fourier filter - whether you want to use a Fourier filter, where the low-r region of the PDF is back-transformed and used to correct the S(Q) for a curved background.<br>
Low-r cutoff - the value to use as rmax for the Fourier filter. Choose a value that does not encroach upon the first real peak in your data<br>
Output file names - your choice of file name. I always include the _ft suffix to ensure that I know what they are in the future!<br>
Final scale number - the sum of the Faber-Ziman partial coefficients for your sample<br>
Output file names - your choice of file name. I always include the _rmc suffix to ensure that I know what they are in the future!<br>
Cutoff, 1st peak min/max - entering 0 0 0 is simplest. Entering 3 1.5 2.5 (for example) will set everything below 3 Å in the PDF to zero, with the exception of the region between 1.5 and 2.5 (which represent the
edges of the first peak). This is to account for major low-r noise which RMCProfile will try to fit if you're not careful, but in practise I don't often use it.<br>
<br>
I hope this is helpful and please do get back in touch if you need further assistance!<br>
<br>
Best wishes,<br>
Helen<br>
<br>
<br>
-----Original Message-----<br>
From: rmcprofile-users [<a href="mailto:rmcprofile-users-bounces@rmcprofile.org">mailto:rmcprofile-users-bounces@rmcprofile.org</a>] On Behalf Of Koch, Rob<br>
Sent: 09 August 2017 20:05<br>
To: rmcprofile-users@rmcprofile.org<br>
Subject: [RMCProfile-users] Help with stog.exe or stog_new.exe<br>
<br>
Hello,<br>
<br>
<br>
In the past I have mostly worked with fitting what some in the community call G(r), but what I believe is called D(r) in the RMCprofile documentation.<br>
<br>
<br>
I'm interested in testing out RMCprofile and I've been told I can use a tool called stog (S to G) to convert from the total scattering structure function to a PDF of a form compatible with RMCprofile.<br>
<br>
<br>
I cannot however find any documentation on this tool, and while the prompts are mostly self explanatory, the tool crashes after prompting me for "add values:"<br>
<br>
<br>
Any advice is appreciated!<br>
<br>
Thanks,<br>
<br>
Rob Koch<br>
<br>
<br>
<br>
Robert J. Koch, PhD<br>
Post-Doctoral Research Scientist<br>
Alfred University<br>
New York State College of Ceramics<br>
Inamori School of Engineering<br>
Alfred, NY 14802<br>
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