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cdf function in rdf.InterRDF_s does not give cummulative distribution function #130

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VOD555 opened this issue Jul 11, 2020 · 1 comment
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@VOD555
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VOD555 commented Jul 11, 2020

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

@VOD555 VOD555 added the bug label Jul 11, 2020
@VOD555 VOD555 self-assigned this Jul 11, 2020
@VOD555 VOD555 mentioned this issue Jul 15, 2020
@orbeckst orbeckst added this to the 0.4 milestone Jul 15, 2020
@VOD555
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VOD555 commented Aug 23, 2020

In MDAnalysis, we change the defination of option density (MDAnalysis/mdanalysis#2812). This also needs to be fixed.

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