New virtual method for Actions which is called at steps when action is
active just before atoms sharing. This is the right place where Actions
can change their atom requirements. E.g., you can do

class ColvarSomething{
...
void prepare();
}

void ColvarSomething::prepare(){
// take here your decision and eventually change the requested atoms
}

on how to call it. Would it be better to separate parsing tools and Math
tools?

It is now possible to directly obtain a parsed group
of atoms (also with ranges) using:
vector<AtomNumber> g;
parseAtomList("ATOMS",g);

get the timestep and pbc and it's ready to be tested

It is possible to give default parameter also when having const references.

(or something like this) and made more general

This is a dummy class, which however is useful to avoid mistakes in
index/index+1 stuff for atoms. When it is read from input, it is assumed
that the input string contains the "serial" (i+1). In the code, it
is possible to unambiguously access serial or index.

Just use getAbsoluteIndex(i) to get the absolute number of i-th atom.

I do not understand why, but on sp6 asynch communication is not very
efficient. For mroe then 10 processes, I switch on an old-style
allgather based atom sharing.

I fixed some problem and added virial components. Still I do dot
understand the reason for a small but visible disagreement in
numerical components of the virial

getClosePairs to get the indexes in the positions array, getClosePairsAtomicIndex to get the atomic indexes instead

Add a class for NeighborList between two lists of atoms. Still experimental and probably not working.

Just a tool to convert strings in the form "10-13"
to arrays of strings as 10,11,12,13.
Still it is not used in currently implemented CVs

To retrieve the timestep and to retrieve the periodicity

(See the user manual).
I also fixed some small error in its documentation.

Now it has to be built from /imd, and loaded as a shared
library with LOAD .../libimd.so in the plumed.dat file

I also change the user-doc script so as to document also .cpp from
other directories (such as imd)

PI,2PI,-PI,-2PI,+PI,+2PI, available wherever a double is parsed