Notice that almost all files were updated with the astyle commit
2813d759

Year in header is here updated to 2017

This is a huge commit, applying indentation to the whole
code. Notice that this commit is made on master branch
after having merged with -s ours from branch v2.3

See #215

This is a huge commit, applying indentation to the whole
code.

See #215

Given header file.h, it is good practice to have a file file.cpp
that includes it as first header.

I just fix the order of includes here. There are still several
headers which do not have a corresponding cpp file, and also
a few that are not included anywhere (which is obviosuly an error).

I will fix them in a later commit.

Added weighting in symmetry functions so you can calculate things like coordination number between atoms that are three coordinated

Using common routines for input of atoms across all MultiColvars, MultiColvarFunctions and AdjacencyMatrices

Partial task lists are now reallocated at the start of each step.  In addition,
only active colvars are stored in storeDataVessels

The neighbour list in these actions never really worked and
anyway with the link cell business it was made rather obsolete.
I am doing this now because I am trying to run very large systems
and need to cut down on memory usage

This makes the combination of Q6+LQ6+VOLUMES faster as you only
calculate the Q6 values in the region of interest and the surrounding
link cells.  In other words you avoid calculating things that you know
will make no contribution to the CV

This change makes it possible to calculate the average x component
of a the vector defining the orientation of a molecule by using something like
MOLECULES MOL1=1,2 MOL2=3,4 MEAN={COMPONENT=2}

Now during the first loop through the calculation of a multicolvar
function only the value is calculated.  The calculation of the derivatives
is avoided.  This will probably save some computational expense if you are
using local_q6.  For regular q6 it does not save much cpu time.

@gtribello please check