def test_same_result(sels, n_blocks):
# should see same results from analysis.rdf and pmda.rdf
s1, s2 = sels
nrdf = rdf.InterRDF(s1, s2).run()
prdf = InterRDF(s1, s2).run(n_blocks=n_blocks)
assert_almost_equal(nrdf.count, prdf.count)
assert_almost_equal(nrdf.rdf, prdf.rdf)
def test_trj_len(sels, step):
# should see same results from analysis.rdf and pmda.rdf
s1, s2 = sels
nrdf = rdf.InterRDF(s1, s2).run(step=step)
prdf = InterRDF(s1, s2).run(step=step)
assert_almost_equal(nrdf.n_frames, prdf.n_frames)
assert_almost_equal(nrdf.rdf, prdf.rdf)
def test_range(u):
s1 = u.atoms[:3]
s2 = u.atoms[3:]
rmin, rmax = 1.0, 13.0
rdf = InterRDF(s1, s2, range=(rmin, rmax)).run()
assert rdf.edges[0] == rmin
assert rdf.edges[-1] == rmax
def test_reduce(sels):
# should see numpy.array addtion
s1, s2 = sels
rdf = InterRDF(s1, s2)
res = []
single_frame = np.array([np.array([1, 2]), np.array([3])])
res = rdf._reduce(res, single_frame)
res = rdf._reduce(res, single_frame)
assert_almost_equal(res[0], np.array([2, 4]))
assert_almost_equal(res[1], np.array([6]))
def test_cdf(sels):
s1, s2 = sels
rdf = InterRDF(s1, s2).run()
cdf = np.cumsum(rdf.count) / rdf.n_frames
assert_almost_equal(rdf.cdf[-1], rdf.count.sum()/rdf.n_frames)
assert_almost_equal(rdf.cdf, cdf)
def test_double_run(sels):
# running rdf twice should give the same result
s1, s2 = sels
rdf = InterRDF(s1, s2).run()
rdf.run()
assert len(rdf.count[rdf.count == 3]) == 7
def test_count(sels):
# should see two distances with 7 counts each
s1, s2 = sels
rdf = InterRDF(s1, s2).run()
assert len(rdf.count[rdf.count == 3]) == 7
def test_count_sum(sels, scheduler):
# OD1 vs OD2
# should see 577 comparisons in count
s1, s2 = sels
rdf = InterRDF(s1, s2).run()
assert rdf.count.sum() == 577
def test_nbins(u):
s1 = u.atoms[:3]
s2 = u.atoms[3:]
rdf = InterRDF(s1, s2, nbins=412).run()
assert len(rdf.bins) == 412
def test_exclusion(sels, exclusion_block, value):
# should see 397 comparisons in count when given exclusion_block
# should see 577 comparisons in count when exclusion_block is none
s1, s2 = sels
rdf = InterRDF(s1, s2, exclusion_block=exclusion_block).run()
assert rdf.count.sum() == value