GR (Module)
Overview
The RDF
module calculates a full set of partial radial distribution functions, $g_{ij}(r)$ for each unique pair of atom types $i$ and $j$ present in the target configuration(s).
The RDF
module is designed to calculate the necessary input for other modules such as
SQ - there is no facility for calculating other types of radial distribution function, e.g. those between the centres-of-mass of molecules. To calculate such quantities see the analysis modules.
Description
For a configuration containing $N$ distinct atom types there are $\frac{1}{2}N(N+1)$ unique partial radial distribution functions $g_{ij}(r)$, where $i$ and $j$ are the $i^{th}$ and $j^{th}$ atom type respectively. The standard formalism for a radial distribution function between atom types $i$ and $j$ is
$$ g_{ij}(r, \Delta r) = \frac{n_j(r,\Delta r)}{\frac{4 \pi}{3}[(r+\Delta_r)^3 - r^3]\rho_j} $$
where $g_{ij}(r, \Delta r)$ is calculated for a spherical shell with inner radius $r$ and thickness $\Delta r$, $n_j(r, \Delta r)$ is the number of particles of type $j$ within the shell, and $rho_j$ is the bulk number density of $j$ over the whole configuration. $g_{ij}(r)$ therefore represents the discretised probability of finding an atom of type $j$ at a distance $r$ from the central atom type $i$, relative to the probability of finding one assuming a uniform distribution of $j$ throughout the simulation box.
Options
Targets
Keyword | Arguments | Default | Description |
---|---|---|---|
Configuration |
Configuration |
– | Required Target configuration on which to operate. |
Range
Keyword | Arguments | Default | Description |
---|---|---|---|
BinWidth |
delta |
0.025 |
Bin width (spacing in $r$) to use |
Range |
r |
15.0 |
Maximum $r$ to calculate $g(r)$ out to, unless UseHalfCellRange is true |
UseHalfCellRange |
bool |
true |
Whether to use the maximal RDF range possible that avoids periodic images. If true then the radius of the inscribed sphere for the configuration box is used as the limit. |
Averaging & Smoothing
Keyword | Arguments | Default | Description |
---|---|---|---|
Averaging |
int |
5 |
Number of historical partial sets $n$ to combine into final partials |
AveragingScheme |
AveragingScheme |
Linear |
Weighting scheme to use when averaging partials |
|IntraBroadening
|Function1D
|Gaussian
|Type of broadening to apply to intramolecular $g(r)$|
|Smoothing
|int
|0
|Degree of smoothing $n$ to apply to the calculated $g(r)$, where $2n+1$ controls the length in the applied Spline smooth|
Export
Keyword | Arguments | Default | Description |
---|---|---|---|
Save |
bool |
false |
Whether to save partials and total functions to disk. Separate files are written for each partial between atom types $i$ and $j$, as well as the total. Files are named after the configuration from which they were calculated. |
SaveOriginal |
bool |
false |
Whether to save original (unbroadened) partials and total functions to disk. Separate files are written for each partial between atom types $i$ and $j$, as well as the total. Files are named after the configuration from which they were calculated. |
Advanced
Keyword | Arguments | Default | Description |
---|---|---|---|
InternalTest |
bool |
false |
Perform internal check of calculated partials against a set calculated by a simple unoptimised double-loop |
Method |
Simple |Cells |Auto |
Auto |
Calculation method to use. All available methods give the same results, but are suited to specific sizes of system. |