Wrong rdf values from InterRDF_s when given 'density=True'

[VOD555]

Expected behavior

If we set density=True, the results from rdf.InterRDF_s should be the same as rdf.InterRDF when given a single-atom to single-atom pair.

See also MDAnalysis/pmda#120

Actual behavior

The results from rdf.InterRDF_s will be 1/N of rdf.InterRDF.
Where N = nA * nB, and nA, nB are the number of atoms in atomgroup A and atomgroup B.

Code to reproduce the behavior

import MDAnalysis as mda
from MDAnalysisTests.datafiles import GRO_MEMPROT, XTC_MEMPROT
from pmda.rdf import InterRDF_s
from MDAnalysis.analysis import rdf

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]]

rdfs = InterRDF_s(u, ags, density=True)
rdfs.run()


ref_s1 = u.select_atoms('name ZND and resid 289')
ref_s2 = u.select_atoms('name OD1 and resid 51 and sphzone 5.0 (resid 289)')
ref_rdf = rdf.InterRDF(ref_s1, ref_s2, density=True)
ref_rdf.run()

from numpy.testing import assert_almost_equal

assert_almost_equal(rdf_ref.rdf, rdfs[0][0][0])

Current version of MDAnalysis

• Which version are you using?
  MDAnalysis1.0.0
• Which version of Python?
  python 3.6
• Which operating system?
  Ubuntu 18.04