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

Naming is now consistent with other functions such as
getGlobalForces, modifyGlobalVirial, etc

See #357.

The whole code, including optional modules, correctly compiles
indicating that this function was used in a single place.

In case some foreign code uses getPosition(AtomNumber), after this
update the compilation will fail (and will not just produce incorrect results).
So I think this change can be merged safely.

Using c++11 to have constructors of generic size.

Two types of optimization implemented:

1. Tensor is used instead of Matrix. This allows avoiding the extra
allocations required in Matrix to setup the workspace, since the
needed space is now on the stack rather than on the heap

2. When align==displace, only lower eigenvalue is computed.

Overall, these changes result in a 5-10% speedup of rt46 on my mac

I used Tensor/Vector operations now

Notice that one can provide an evec matrix with less rows.
In this case, the lower eigenvalues will be found. In addition,
temporary data is on the stack (array) rather than on the heap (vector),
making it faster for small matrices.

see 7a72bc37

Using completion the config.sh script is called during compilation.
This fix avoids problems when cltools is compiled before config

One could just use a plain object in these cases (no pointer)
but I did the minimal change to remove the delete statement.

This reverts commit d190c105.

This reverts commit 40099475.

This reverts commit 14eb6054.

This reverts commit 8e6a72aa.