This commit contains changes automatically generated by plumedbot on Travis-ci.

I replaced a few pointers with vectors or arrays

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.

style warnings

I removed the NOPBC key from manual (it is not used)

[makedoc]

I set it to 2 instead of 2.0, so that it will not be necessary
to update it

I replaced everywhere it made sense the new Communicator class
syntax. This commit is not strictly necessary, but provides
examples of the simpler syntax so I think should be merged

Now the stride for the neighbor lists in the path implementation
are in timesteps. By now this means that PATHMSD and PROPERTYMAP are
defined with e.g. NEIGH_STRIDE=5

Now the code crashes in the following cases:
1. An exchange is attempted on a step where neighbor list for COORDINATION
(or DHENERGY) are not updated
2. An exchange is attempted and neighbor list for PATHMSD or PROPERTYMAP are enabled.

The second should be fixed better to allow using strides for lists which are
divisor of the stride between steps. The better thing will likely come later, at least
the code is safe now.

Mostly unused variables