This fixes a problem in the way atoms are setup for calculations where you take an input
from a multicolvar filter as input to a new multicolvar if SPECIESA and SPECIESB are used.
For instance you might be calculating Q6 for those atoms that have a coordination number
greater than 4

[makedoc]

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

Year in header is here updated to 2017

File was inconsistent with action and class name

* Added R_POWER option to multicolvar/CoordinationNumber

This is to allow the coordination number moments from White and Voth
2014 JCTC and subsequent papers. They are used as a scalar proxy for
biasing radial distribution. Regtest and CHANGES line have been added as well
as the function/documentation.

(master only)

[makedoc]

(v2.3)

[makedoc]

I added several examples with plumedfile, so I only
push this on master branch.

Fixed #229

This ensures that steinhardt parameters are calculated correctly even if bond
vectors run parallel to the z axis

Allow passing a single trajectory to driver --multi.
The same logic is implemented as in IFile tool, that is:
- look for file.##.ext
- if it does not exist, look for file.ext

Here ## is the replica index and .ext the extension of the file

Fixed #228

[makedoc]

I replaced
verbatim
endverbatim
with
plumedfile
endplumedfile

in (hopefully) all the places where it was appropriate.

Addresses #226

[makedoc]

[makedoc]

MOLTYPE is actually not needed in practice.

[makedoc]

For a few actions that typically write long lists,
I fixed the format to write only 25 fields per line.

Travis-ci job doing cppcheck also checks whether astyle
has been enforced.

See #215

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