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

[Koch, Rob]

Hi Helen,


Thanks for the help, and sorry for my delay.


So I've been playing with 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.


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.


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.


Thanks again!

Rob


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

________________________________
From: rmcprofile-users <rmcprofile-users-bounces at rmcprofile.org> on behalf of helen.playford at stfc.ac.uk <helen.playford at stfc.ac.uk>
Sent: Tuesday, August 15, 2017 11:01:00 AM
To: rmcprofile-users at rmcprofile.org
Subject: Re: [RMCProfile-users] Help with stog.exe or stog_new.exe

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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