compute_rdf#
- compute_rdf(source, type1, type2, cutoff=10.0, dr=0.1, **kwargs)[source]#
- compute_rdf(source, type1, type2, cutoff=10.0, dr=0.1)
- compute_rdf(source, type1, type2, cutoff=10.0, dr=0.1, skip=1)
Calculate the Radial Distribution Function (RDF) g(r), and its derivatives G(r) and n(r).
This function uses singledispatch to handle either a static AtomicSystem or an MDAnalysis Universe (for trajectory analysis).
- Parameters:
- sourceAtomicSystem or mda.Universe
The source structure or trajectory to analyze.
- type1str
Atom type for the first selection (‘all’ or specific type).
- type2str
Atom type for the second selection (‘all’ or specific type).
- cutofffloat, optional
Maximum distance for the RDF calculation (in Angstroms).
- drfloat, optional
Bin width for the histogram (in Angstroms).
- skipint, optional
Number of frames to skip during trajectory analysis (only for mda.Universe).
- Returns:
- pd.DataFrame
Indexed by distance
r, with columnsg_r,G_randn_r.- float
The number density of the second selection, in atoms per cubic Angstrom, that
g_rwas normalised by. Returned because the normalisation is what makes an RDF comparable between systems, and checking it is the quickest way to tell a real first peak from one produced by the wrong particle count.
- Raises:
- TypeError
If the provided source type is not supported.