Add a method to extract some states of the particles -- extractParticlesState(0,3) should return the positions

Ensure that the limit will not be included in the interval -- Add an assertion if a dead lock will appear

Sampled position is different from checkpoint position, I still need to
fix that.
However, there's another issue that needs to be solved first

This reverts commit b4bbc44b.

This reverts commit 6c803fa1.

This reverts commit f843c813.

Debug -- add default value for cutoff and options -- use different tag values to be idle if missmatch

a lot easier to read now

the "simname_particles.h5" file is now only opened once, and then
samples are written the same as before.
some sanity checks of the velocity and acceleration data should still be
performed.

Make it compile, but I would have prefer a class attribute instead of method to decompose template of field

for linking against some particular libraries, it's necessary to add
"extra_libraries" such as '-Wl,--start-group'.
Therefore when the compile command is now constructed, "extra_libraries"
are checked to see whether they start with '-' or '/' (for static
libraries given as full file names).