Open VOD555 opened 4 years ago
cdf function returns cummulative distribution function between particles A and particles B.
cdf
cdf function returns cummulative number density of particles B in a shell at distance r around a a particle.
r
a
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()
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.
density
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 distancer
around aa
particle.Code to reproduce the behaviour
Currently version of MDAnalysis:
MDAnalysis 1.0.0 pmda 0.2.1