Here are some changes to all spheres nonbonded list to fix a bug that
Frido found as well as make things faster. The nonbonded lists now have
checks built into them so asserts should fail if anything goes wrong.
Note that these checks are very expensive for large numbers of particles
(quadratic) and so any real runs with IMP should use builds with NDEBUG
defined. We may want to define macros like IMP_CHECK_EXPENSIVE to
provide finer grain control over debugging checks.
Note: you can say "scons release=true" to turn off most debugging
checks. But the nightly builds use the default (release=false) since we
need all the testing we can get right now.
BTW, the Frido-sphere test doesn't seem to contain any assertions, so
I'm not sure what it's supposed to test (although the particle
coordinates seem rather precise). Is it supposed to crash without this
patch? (It seemed to work fine on synth without it.) If so, a comment in
the test case saying something like "causes a segfault with r456 or
older due to a bug in foo" would prevent future people from deleting the
seemingly useless test.