In particular, I would like to be able to just do the
"forward" loop (calculate()) and not the "backward" loop
(apply()). In this manner, when computing foreign biases
for acceptance in replica exchange, I will only call the
forward loop, which computes colvars and biases. Clearly,
we should move printing/analysis/hills-adding stuff
outside the "calculate" method, so as to avoid doing these
things in the acceptance calculation. I wait for this further
cleaning since, until replica exchange is not actually there,
there is no practical difference. Also, we may decide to change
a bit the name of methods (calculate/apply are becoming a bit
misleading?)

Instead of deactivating actions at the end of the step, I prefer
to deactivate all of them just before activation. In this manner, all
dependencies are touched in the prepareDependencies method.

It is a very primitive "serialization" interface. I just put it here
so as to use it with replica exchange to send atoms to other replicas.
Still, we should plan something more general than this and replace it,
especially when we will need to pass between replica more complex objects.

This will be necessary for replica exchange

I also removed an "included" added by Davide a few commits ago. I think
it should not be here, but if it is necessary on some compiler we can
reinsert it. However, we should use "cstring" and not "string.h"

wrong behavior with mpi-plumed+non-mpi-md

I modified the "LOAD" command in such a way that if one
writes "LOAD pippo.cpp" in the plumed.dat file, pippo.cpp is automatically
compiled to a pippo.so which is then loaded.

A compile_options.sh file is generated by make in the src directory
and it is used to properly compile a .cpp into a .so (or .dylib on mac).
Just type "plumed mklib pippo.cpp". Still it should be improved in term
of linking of multiple .cpp files.

Modified the "plumed" script so as to simplify the addition of new
tools. To add a new tool just put a script in tools/scripts with extension
.sh. The script should understand the keyword "--description" which is used
to build a summary of available scripts in the main "plumed" script.

Groups are removed when GenericGroup objects are deleted

Dependencies are not generated when cleaning

Fixed a bug which was giving nan when distances with pbc were
computed in boxless systems.

There was a wrong call in the access to units

(valgrind)

Especially, I removed "0" atoms, which was always crashing.
I also put some example of groups and centers of mass

I also replaced math.h with cmath

Part of the interpretation of the cmd string can be moved here.
Also, it will be easy to define other classes with this interface
(I am planning to do that for gromacs-style replica exchange)

I prefer not to use strtok_r, which is not standard, not strtok, which
is not thread-safe.

Added some doc and removed declaration of an unused function

not using splines

file are still missing. And probably needs optimization (inline stuff?)

to having Grid and SparseGrid class and a flag dospline

cubic splines (from plumed1 at this time). At variance with Grid,
an additional vector<double> containing derivatives should be
provided when using the methods addValue and setValue.
The method getValue can be called with or without requesting derivatives.
The second class SparseGridWithSpline inherits from SparseGrid and
implements the splines in an analogous manner.

I forbid Actions to declare both an unnamed value and named values.
In a far future, the action name alone will imply passing the full structure.
Example:
d1: DISTANCE ATOMS=1,2 COMPONENTS
now only declared d1.x d1.y and d1.z, whereas d1 cannot be accessed
directly as a value (since it is a complex structure that we cannot handle
yet)

I moved all units conversion factor into a separate object.
This slightly simplify the code and allows to easily
introduce new conversion factors (e.g. for charges).

A group can be creating using GROUP directive. Groups
are then automatically expanded when their name is found in parseAtomList.

This is to be sure that requestArguments() and requestAtoms()
are only called from the right place, i.e. prepare()
or initialization