…nalysis. Before, all frames were loaded (and selection was always applied). Now, the frames which are not used are not loaded, thus improving the performance. This only happens when the step is larger than the tau_max + 1.

Test cases cover the situation where some frames are skipped. The test checks how many times the 'select_atoms' was called.

This is to help with the large size MD simulations analysis.

 was set up or not. Also, manually moving between the frames rather
 then using "for _ in trajectory[]". This removed unnecessary variables.

border condition for "tau_max" and "step".

patch.

which atoms are found.

as a gap: meaning that setting it to the value of 2 means that the atom
id 7, when in the sequence 7,X,X,7, where X means absence, will be
rewritten to 7,7,7,7. This way the intermittency does not affect the
actual routines for SP calculation. The array of IDs should never
be big so this should not add any significant computational time.

to the selected IDs, using the selected IDs to verify the behaviour of
the intermittency.

parameter is complex and was accounted for here, together with new
test cases. If necessary, we load extra frames for each window,
to account for the borders: for the first and last frame in a window.

analysis. This requires several runs and averaging.

…usz/mdanalysis into bieniekmateusz-survival_probability

…usz/mdanalysis into bieniekmateusz-survival_probability

…alysis into survival_probability