[RMCProfile-users] Help with stog.exe or stog_new.exe

Tue Aug 15 16:01:00 BST 2017

Hi Rob,

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.

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.

Number of files to include 	- this is a throwback to a previous incarnation of the program, and should be 1
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
Q min and max			- as it sounds
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) 
x-offset			- this should be half the histogram bin width
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!
Maximum r 			- your choice, e.g. 40
Number of r points		- ideally the number that gets you an r-spacing of 0.02, e.g. 2000
Window function y/n?		- whether or not you want to use the Lorch function (should usually be no)
Number density		- must match whatever simulation box you are going to use, e.g. the crystallographic density
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
Try again			- can try a different small offset by entering it here, or just say no to move on
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.
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
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!
Final scale number		- the sum of the Faber-Ziman partial coefficients for your sample
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!
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.

I hope this is helpful and please do get back in touch if you need further assistance!

Best wishes,
Helen

-----Original Message-----
From: rmcprofile-users [mailto:rmcprofile-users-bounces at rmcprofile.org] On Behalf Of Koch, Rob
Sent: 09 August 2017 20:05
To: rmcprofile-users at rmcprofile.org
Subject: [RMCProfile-users] Help with stog.exe or stog_new.exe

Hello,

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.

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.

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:"

Any advice is appreciated!

Thanks,

Rob Koch

Robert J. Koch, PhD
Post-Doctoral Research Scientist
Alfred University
New York State College of Ceramics
Inamori School of Engineering
Alfred, NY 14802
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