[RMCProfile-users] Separation between functionally different atoms

[Wojciech Slawinski - UKRI STFC]

Dear Tilan,

Thank you for using RMCProfile. It is indeed a bit confusing but currently, data2config cannot distinguish Oxygens  from different crystallographic sites. Once you start swapping atoms, you will have those mixed in between the sites.



The solution to this, is to call your Ow another atom type. You can choose what you like. The extra line in the *.dat file will be NEUTRON_COEFFICIENT (I know it is really confusing) as described in the manual, using a correct number of electrons for an extra atom type.



If you have any other questions, you can email me directly.

Good luck,

Wojciech Slawinski

Chemistry Department,

University of Warsaw, Poland

wslawinski at chem.uw.edu.pl




________________________________
From: rmcprofile-users <rmcprofile-users-bounces at shadow.nd.rl.ac.uk> on behalf of Tilman Grünewald <tilman.grunewald at fresnel.fr>
Sent: 07 February 2019 16:54:35
To: rmcprofile-users at rmcprofile.org
Subject: [RMCProfile-users] Separation between functionally different atoms

Dear all,

I am using X-ray PDF to investigate the structure and transformations in amorphous Calcium carbonates in biological systems. What I would like to do is very much alike to Andrew Goodwin et al., Chem Mater 2010. It is also this paper that led me to RMC Profile for my analysis. Thanks to the good documentation and the tutorials I got started very quickly. I am really appreciating such great documentation and would like to thank you for that!

I am now trying to create the structure of Monohydrocalcite in to a rmc6f file and trying to preserve the functionally different oxygens as separated atoms.
I am working with a cif file that gives the different positions in the following way

_atom_site_U_iso_or_equiv
Ca   0.27690   0.00000   0.33333   1.00000   0.01558
C   0.71880  -0.02610   0.36360   0.50000   0.01431
O1   0.45600   0.27440   0.06960   1.00000   0.02026
O2   0.06910  -0.05040   0.78560   0.50000   0.02482
Ow   0.60270   0.00000   0.83333   1.00000   0.02229
H   0.55200   0.09500   0.91600   1.00000 ?

So I have a split occupancy on the C/O2 site as well as the Ow from water that I would like to keep separated from the Calcite Oxygen. If I generate a config file with data2config, I can preserve the vacancy but the oxygens are mixed up. I found a discussion between Romain Sibille and Helen Playford from Sept 2016 which comes close, but I don’t understand the solution Helen suggested and how that keeps the atoms separated. Some hints on how to handle this would be very much appreciated :)


Thanks a lot and best regards
Tilman
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