[ase-users] Radial Distribution Function

[Maxime Van den Bossche]

Dear Amarjit,

I didn't implement this function, but I had a look at
the code and to me it seems correct, and also
corresponds to the formula you provided (though
with a more precise determination of the 'shell
volumes' in the normalization).

The documentation could perhaps be a little improved
though. The implemented scheme is the standard
one used for extended systems. For e.g. isolated
nanoparticles or gas-phase molecules, one would
normally not use the number density in the normalization
(since the volume is ill-defined). And for extended systems,
one also should make sure that the cell encloses a sphere
with radius rMax, and one then also needs to provide
a distance matrix calculated within the minimum image
convention, otherwise some neighbours will not get
counted. I will open a merge request on this later today.

Best,
Maxime


Op zo 11 aug. 2019 om 12:00 schreef <ase-users-request at listserv.fysik.dtu.dk
>:

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>    1. Radial Distributional Function (A Singh)
>    2. Re: Potential Pubchem API Integration (Ask Hjorth Larsen)
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> Message: 1
> Date: Sat, 10 Aug 2019 17:04:46 +0100
> From: A Singh <a.singh.2313 at gmail.com>
> To: ase-users at listserv.fysik.dtu.dk
> Subject: [ase-users] Radial Distributional Function
> Message-ID:
>         <
> CAFn314c5rF4CXHqH5xGH4V-EKNgospfECeeGmPqzy8jpcGfEEQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I've been using the get_rdf() function from ase/ga/utilities.py and have
> noticed that the formula for calculating radial distribution is not the
> same as found in computational chemistry books. The correct formula I
> believe is:
> *g(r)=n(r)/(Nr 4p r**2**Dr)*
> In which *g(r)* is the RDF, *n(r)* is the mean number of atoms in a shell
> of width D*r* at distance *r*, r is the mean atom density, *N * is the
> total number of atoms.
> It would be great if someone could explain what has been implemented in
> get_rdf().
>
>
> Thanks,
>
> Amarjit Singh Gaba
>
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