[makedoc]

this is for plumedcheck

[makedoc]

[makedoc]

collectEnergy is a bool and was initialized to 0.0.
That is equivalent to false, so it works correctly,
but does not make much sense.

[makedoc]

for 1D flexible bins (usefull for PBMetaD)

[makedoc]

I backported the optimized tools/Torsion.cpp from v2.3.

This implementation avoids taking inverse of numbers that could be zero.

* Marco De La Pierre: PBMetad with HILLS written on disk

* Marco De La Pierre: updated regtest for PBMetad with HILLS on disk

These two tests needed changing because periodicity was not incorporated correctly
in the KDE estimation previously.  As such the outputs given were wrong previously.
The previous changed incorporated the periodicity correctly.  This change is thus
required as a result.

Partial tempering/gromos