[RMCProfile-users] X-ray PDF use

[Kuo Li]

Dear all,

I have a question about using polyhedral constraints.

I collected neutron PDF data of an amorphous hydrocarbon sample (no obvious
peak above 15-20A in G(r)), which is believed to be linked
polyaromatichydrocarbon. I hope to fit it starting from the model of
Benzopyrene or anthracene, etc (or even a mixture of them). Does anyone
know how to make a restraint to keep the molecule (Benzopyrene or
anthracene) rigid?

Thank you very much!
Kuo


On Fri, Dec 6, 2013 at 10:40 AM, <matt.tucker at stfc.ac.uk> wrote:

>
>
> Dear Christopher,
>
>
>
> 1)      Can RMCProfile fit x-ray PDF?: Yes
>
>
>
> What Chris Kerr says is not strictly true. RMCProfile can fit x-ray PDF
> data.
>
>
>
> The x-ray F(Q) can be fitted with the XRAY_RECIPROCAL_DATA keyword.
> However, the x-ray form factors have to be in the data file and it has to
> be convolved with the simulation box size. There is a program call
> xray_to_rmc that will do this for you if supplied the data in the usual rmc
> format.
>
>
>
> For the x-ray PDF, since the q-dependant part has been divided out you can
> treat this as a neutron PDF with different weights. These weightings are
> defined using the keyword NEUTRON_COEFFICIENTS (sorry a bit confusing I
> know).
>
>
>
> We are writing a tutorial example to show how all this works and it will
> be in the minor update 6.5.2. This will be out in the next few weeks.
>
>
>
> As Chris Kerr says there are plans to fit the x-ray PDF in a more rigorous
> way. Once this is implemented it will be useful for all x-ray PDF data, as
> it will make a fairer comparison regardless of the atomic radii
>
>
>
> 2)      How do you fit nanoparticles with RMCProfile?
>
>
>
> Sadly this is not an easy question to answer, there are three possible
> approaches.
>
> a.       The first is to treat the data as a bulk sample if the particle
> is large. If not then a modification function for the particle size could
> be applied but this isn’t implemented at present.
>
> b.      The second (as Chris says) is to put one particle in a large box
> and only fit out to a distance where it does not see its periodic repeat
> (RMC uses periodic boundary conditions).
>
> c.       Finally if you can build a starting configuration with particles
> in a matrix that is not too large (> ~40,000 atoms), then you can use the
> various constraints/restraints to hold things together and model it as
> normal. This of course is not trivial but probably the ideal solution.
>
>
>
> If you tell us some more about your system we can advise what your best
> approach is most likely to be.
>
>
>
>
>
> Best wishes,
>
> Matt
>
>
>
>
>
> .
>
>
>
>
>
>
>
>
>
>
>
>
>
> *From:* rmcprofile-users-bounces at rmcprofile.org [mailto:
> rmcprofile-users-bounces at rmcprofile.org] *On Behalf Of *Christopher J.
> Wright
> *Sent:* 02 December 2013 00:36
> *To:* rmcprofile-users at rmcprofile.org
> *Subject:* [RMCProfile-users] X-ray PDF use
>
>
>
> Hi,
>
> I am working with PDF data collected from an x-ray synchrotron source.
> The samples are nanoparticles of various size and compositions.  Is it
> possible to model these particles using RMCprofile?
>
> Thank you very much,
>
> Christopher J. Wright
>
> Brown University Chemistry Department
>
> --
> Scanned by iCritical.
>
>
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> rmcprofile-users at rmcprofile.org
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>
>


-- 
Kuo Li
Joint Insitute for Neutron Science
Oak Ridge National Laborotary
Carnegie Institution of Washington
Office:865-241-3114
Mobile:301-335-2187
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