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Clarification on one option that does not work on BG/Q

Now when plumed is installed the scripts are placed in
lib/plumed/
instead of
bin/

This makes it more robust the installation of several versions with suffixes

I only left in place the script "plumed-patch" which is likely
the most used.

I added plenty of messages at the end of ./configure and make install
+ I explained it in the user doc

Using "_" instead of "-" to avoid clashes.

Actually, the problem was that doing
make install PLUMED_SUFFIX=2
make install
The second install would have canceled the executables installed
by the first install. This is because install assumes names such as
plumed-* to be scripts installed for cross compiling

We usually allowed users to customize the name of the plumed
library using env var PLUMED_LIBSUFFIX. I changed it to the
standard autoconf behavior, that is using
--program-suffix
--program-prefix
at configure time.

PLUMED_LIBSUFFIX still works but is now deprecated and dumps a warning.
I will convert it to an error in a later version (2.3).

This makes it compatible with the standard behavior of GNU tools.

PLUMED_PREFIX still works but is now deprecated and dumps a warning.
I will convert it to an error in a later version (2.3).

[makedoc]

[makedoc]

[makedoc]

Added PDF manual. I had to reorganize a bit the documentation to make
it more linear. In particular, I assigned each of the previously
"dangling" pages as subpage of another one (e.g. DEBUG keyword).
Additionally, I changed a bit the way MD-specific instructions are linked
and added some comment about the PDF manual in the introduction.

The most important change is that I am not using the Layout anymore since
it was difficult to keep it in sync. Now, in the html version, only
the left-side tree is visible, and the tabs disappeared. I don't think
this is a big issue but we might try to solve it.

PDF manual is still a bit buggy: some links are not properly resolved
and images are not shown. I think we can solve these issues later.

Addresses #101

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.

I have noticed that on some machines one needs to add  -lgfortran
to link blas and lapack correctly (manual updated).

Ready for merge. Nothing should change with existing Makefile.conf.

One can now produce a Makefile.conf and a sourceme.sh
using autoconf. Just type:

./configure

Or maybe

./configure CXX=icpc

In case you want to use mpi, just use:

./configure CXX=mpic++

Everything should be smooth. I took care that the generated Makefile.conf
is compatible with those stored in configurations/. In this way,
one can always resort to a saved configuration file. Moreover,
jumping between git branches (without need of reconfiguring) will be
easier.

More info on the manual page (no need to use autoconf to compile
the manual and see that page)

Closes #46

To be consistent with the paper, plumed is always capital letters.
I also changed 2.0 -> 2 and 1.0 -> 1 for sake of generality

This is the standard path for linux distribution. Thus "make install"
will fail unless run with root permission or unless PLUMED_PREFIX is
explicitly set. I also fixed DYLIB path for mac (plumed path
should be prepended)

Fixes #7

the parts that are contained in the code