It was not doing proper center-of-mass fitting. Now it also implements
the case with displace!=align. Corresponding regtest has been fixed,
and rt14 has been slightly changed (with new numbers it was not meaningful).

It is automatically used whenever it is expected to produce
results identical to the old version. Thus, old version is still used
only when align!=displace or when not all align!=0 are identical

It is still possible to enforce non-safe (faster) version with
OPTIMAL-FAST.

TYPE=OPTIMAL is the old version
TYPE=OPTIMAL-FAST is the new version

Notice that the new version only works with align==displace.
Also notice that old/new version give inconsistent results when weights which are not all equal (or zero) are used. This is something that will be fixed
soon in the old version.

The new version is only used in a couple of regtests, since it still have some problem of numerical stability

RMSD re-implemented from scracth for the case where align==displace.
The new routine is much faster, but has some problem of numerical stability
(rt32 is broken). The code is choosing automatically between new version
(when align==displace) and old version (when align!=displace) so as
to allow the latter for e.g. docking. In RMSD.cpp, you can edit these lines:
// set to true one of these to enforce old routine (Davide's) or new one (Giovanni's)
  const bool enforce_old=false;
  const bool enforce_new=false;
to enforce old/new version.

I used cppcheck --enable=all.

operator= did not work correctly. I put an assertion to check it is not
actually used.

I replaced all the "using namespace PLMD" statements with explicit
namespace PLMD{ …… }. This is more clear and simplify the syntax for
defining operators

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

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.

Now the input can be
 RMSD REFERENCE=frame_1.dat TYPE=OPTIMAL SQUARED
this is usefult to reproduce initial path cv behaviour
without passing through an additional function

in terms of the residues for the chains for which one wishes to calculate the distances
from the alpha helical secondary structure.  For these reasons I had to adjust the PDB
parser so that it reads in atom symbol, resdiue and chainID data.  I then I have an
ActionSetup class (MolInfo) that can read and store the data on the various chains inside the
pdb file.  I have that you can calculate the distances from the secondary structure using either
DRMSD (like plumed 1.0) or using Davide's RMSD class.  This required a very small change to Davide's
RMSD class.

Many checks on size() transformed in checks on empty()
(suggested by cppcheck)

Mostly unused variables, implicit conversions, etc

I tried to also add error messages, at least when I knew the meaning
of the assertion...

I eliminated some compilation dependencies among header files.

I think that "FromPDB" is implicit in the fact that the
first argument is of type PDB)

Now should be really working! Remember: good dinner+beer help a lot!

Initial seed for weighted alignment. Need further debug.

I removed scale method from Vector. I think it is
more readable to use the *= operator.

So that the enum is hidden inside the RMSD class
and syntax is more consistent with other classes

Still it is only the RMSD *without* best alignment