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cdf function in rdf.InterRDF_s does not give cummulative distribution function
Expected behaviour
cdf
function returns cummulative distribution function between particles A and particles B.
Actual behaviour
cdf
function returns cummulative number density of particles B in a shell at distance r
around a a
particle.
Code to reproduce the behaviour
import MDAnalysis as mda
from MDAnalysisTests.datafiles import GRO_MEMPROT, XTC_MEMPROT
from pmda.rdf import InterRDF_s
u = mda.Universe(GRO_MEMPROT, XTC_MEMPROT)
s1 = u.select_atoms('name ZND and resid 289')
s2 = u.select_atoms('(name OD1 or name OD2) and resid 51 and sphzone 5.0
(resid 289)')
s3 = u.select_atoms('name ZND and (resid 291 or resid 292)')
s4 = u.select_atoms('(name OD1 or name OD2) and sphzone 5.0 (resid 291)')
ags = [[s1, s2], [s3, s4]]
rdf = InterRDF_s(u, ags, density=True)
rdf.run()
rdf.cdf()
Currently version of MDAnalysis:
MDAnalysis 1.0.0 pmda 0.2.1
In MDAnalysis, we change the defination of option density
(https://github.com/MDAnalysis/mdanalysis/pull/2812). This also needs to be fixed.