[cctbxbb] tst_miller failing

Pavel Afonine pafonine at lbl.gov
Wed Aug 26 14:30:47 PDT 2015


Hi Markus,

I loosened tolerances. Hopefully that fixes the problem, please let me 
know otherwise.

Pavel

On 8/11/15 01:30, markus.gerstel at diamond.ac.uk wrote:
> Hi everyone, particularly Pavel I guess,
>
> I had a look at one intermittently failing test: cctbx/regression/tst_miller.py, run with parameter P31
>
> The relevant piece of code is:
>   def exercise_randomize_amplitude_and_phase():
>     xrs = random_structure.xray_structure(
>       space_group_info=sgtbx.space_group_info(number=1),
>       elements=["C"]*300)
>     fc = xrs.structure_factors(d_min=1).f_calc()
>     def run(a,p):
>       fc_ = fc.randomize_amplitude_and_phase(amplitude_error=a,
>         phase_error_deg=p, random_seed=1312425)
>       d1, d2 = flex.abs(fc.data()), flex.abs(fc_.data())
>       r = flex.sum(flex.abs(d1-d2))/flex.sum(flex.abs(d1+d2))*2
>       return (r, fc.mean_phase_error(phase_source=fc_))
>     #
>     assert approx_equal(run(0,0), (0,0))
>     for v in list(xrange(0,91, 10)):
>       r = run(v/100.,v)
>       assert approx_equal(r[0], v/100., 0.01)
>       assert approx_equal(r[1], v, 1)
>
> The test fails in the last line for varying values of v. I saw that the values of r[] increase proportionally to v, so I ran the test 2000 times for v=90, plotting the values of r[0] and r[1]; results attached.
> With the current statistics the r[1] test is expected to fail in 1 run out of every 80.
>
> Could you please have a look at this, and either increase the tolerance on the test or identify whether these values are true unexpected outliers indicating a problem in the code? Don't know what the r[1] distribution should look like, but that's clearly not normal.
>
> :)
>
> -Markus
>
>
>
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