[RMCProfile-users] Using RMCProfile For X-ray Data of Amorphous Materials

[helen.playford at stfc.ac.uk]

Dear Mostafa,

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.
1-    -The manual doesn’t mention how can create an initial configuration of amorphous materials.
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.
2-   -The manual doesn’t mention how I can fit XRAY_REAL_SPACE_DATA.
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).
3-    - Is the program calculated the x-ray partial structure coefficients like for neutron.
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.
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.
4-    -I use PDFgetx3 for calculating F(q) and G(r),are these data need to rescaled and convolved.
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: http://journals.iucr.org/j/issues/2001/02/00/issconts.html
5-    -When I use rmc326 for converting the old *.dat file to version 6 it give me error that “'rmc326' is not recognized as a operable program or batch file.”
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.
6-    -how can I get atomeye file from rmc configuration file(cfg) in general because in the tutorial you use get_atomeye_sf6 and it if for this example only.
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.



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.

Best regards,
Helen


From: rmcprofile-users [mailto:rmcprofile-users-bounces at rmcprofile.org] On Behalf Of Mostafa Saad
Sent: 07 July 2014 09:37
To: rmcprofile-users at rmcprofile.org
Subject: [RMCProfile-users] Using RMCProfile For X-ray Data of Amorphous Materials

Dear all,
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.

First I follow the manual and tutorial but I face some problems like:

1-    -The manual doesn’t mention how can create an initial configuration of amorphous materials.

2-   -The manual doesn’t mention how I can fit XRAY_REAL_SPACE_DATA.

3-    - Is the program calculated the x-ray partial structure coefficients like for neutron.

4-    -I use PDFgetx3 for calculating F(q) and G(r),are these data need to rescaled and convolved.

5-    -When I use rmc326 for converting the old *.dat file to version 6 it give me error that “'rmc326' is not recognized as a operable program or batch file.”

6-    -how can I get atomeye file from rmc configuration file(cfg) in general because in the tutorial you use get_atomeye_sf6 and it if for this example only.



Thank you in advance

mostafa saad
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