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

This is actually a squash of many commits entirely made
by Gareth.

It adds the possibility to generate a file useful for VIM syntax highlighting.

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}

Changes to the code are there so that I can reference the atoms
page in the descriptions of keywords that read atom numbers.  I also
changed the input to multicolvar functions.  I stopped using the ARG
keyword in these actions and used DATA instead because you are refering
to the data calculated in a multicolvar as opposed to a scalar quantity
calculated by a particular action.

All components now have to be registered in registerKeywords so that
documentation on what componets are available in a given action are
available in the manual.  Currently the code gives a warning if a user
tries to use a component that is not properly described in the manual.
In the future (v2.2) this warning will be replaced by an error.  That
is to say you wont be allowed to use unregistered components.  This is
all described more in #76

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

I have greatly simplified the hierarchy of classes that inherit from Vessel.
Furthermore, I have re-used much of the parsing functionality in Action so as
to make adding a Vessel more like adding an Action. All the changes in regtests are
just because of changes of the names in the header line.

In addition I added functionality so that multicolvar can pretend to be colvars
Multicolvars have value that are always labelled as label.something.
However, in AlphaRMSD etc the default is to calculate the number of
RMSDs that is less than a certain target value.  Furthermore, in the
manual these MultiColvars are listed as colvars.  The multicolvar functionality
inside alpharmsd being a feature for "advanced users".  Hence, to avoid confusion
I added something so that by default the value in alpharmsd etc is just
label.

The guard "ifndef/define" has been updated so as to also include the
module name. This is important as it will allow files with the same name
to be used in different directories. Modification was done automatically
using header.sh - just run it routinely to keep names consistent

All the source code have been moved into subdirectories of src/
Some of these subdirectories are treated in a special manner:
src/wrapper contains the wrappers for MD codes
src/main contains the main.cpp file
src/config contains files generated without compilation,
  just based on configuration info
src/lib is the place where executables and libraries are put
  at the end
src/cltools contains the command line tools
src/tools contains plumed tools (reusable classes)
src/basic contains PlumedMain, Action hierarchy and other basic stuff
src/multicolvar contains MultiColvar stuff
src/imd is the interactive MD (still not totally portable).

Notice that, to allow easy inclusion of .h files from other modules,
I link all the directories in src/ into module directory. In this
way it is possible e.g. to write #include "config/PlumedConfig.h"

See src/README and src/basic/Makefile to understand how inter-module
dependencies are set

Avoid warnings and increase portability

This clarifies a bit the developer doc

Patch adapted from Toni Giorgino.

use "plumed gentemplate --list" to print list of templates
use "plumed gentemplate --include-optional --action PIPPO" to include
 optional keywords for directive PIPPO

Added a tool for generating template versions of the various collective
variables.  This involved changing the secondary structure variables
work (by default you now do LESS_THAN).  In addition, plumed now understands
that atoms can be specified in multiple ways sometimes.

Also changed the developer manual so as to make it easier to find the
tutorials

command line tools easy to document in the same manner as Actions are
easy to document

modular.  It is now easier to remove features of multicolvar and
to add new multicolvar features.  In addition the functionality of
multicolvar is now more reusable.

as suggested by Gareth

I added a PEOPLE file containing list of authors and a script
(src/header.sh) which applies the Licence to all the source files.

It can be applies multiple times (it automatically deletes the present header
and replace it with the new one). Thus, to change the header, edit header.sh
and execute it.

Added funcitonality so that one can restart field cv calculations
Added field cvs for contact maps