It is not possible to use x2 as a variable. In this case,
sqrt of distance won't be computed.

Actions are now shown in order also when they are more than 10.
Perhaps should be cleaned up a bit, but it works.

Also this after a discussion with @marcodelapierre

thanks to @marcodelapierre

valgrind reported usage of this as an uninitialized value, so I set
it. However, looking at the code below it looks harmless.

This reverts commit 2128bada.

Giving false positive in master branch - no idea why and cannot debug it

This reverts commit 5ba9eb93.

- when using NAMD-like interface, also update the unique list of atoms.
- moved g2l out of dd, since it is also needed when not using MPI
  (in NAMD-like interface)

Partly implemented by @hanatok, see #359

Changed so that start()/stop()/pause() return *this.
This allows things like
sw.start().stop()

Stopwatch can be initialized with the reference to a log. In this
case, it logs itself at destruction, provided the log is open.

Added Stopwatch::Handler class
It allows writing exception safe stopwatches which automatically
stop when an exception is caught.

Removed unnecessary start/stop in PlumedMain constructor.

Simplified interface: Use default arguments instead of multiple functions.

Notice that files are closed on destructor anyway.

Fixes #357

Moved __DATE__ and __TIME__ to config/Config.cpp