Lattice reduction is used in plumed to convert box to its
"least skewed" form. I changed a bit the threashold since it
was giving problems with high optimization flags.
Additionally, I added some warning when too many iterations
are performed (which indicates a numerical issue)

reduced precision to make them work with stronger optimizations

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It seems that sometime on travis a regtest with mw-mpi crashes.

I think this is because when using multiple processors per walker
there is a problem in the opening of the old file (for read) and
its backup (for write). Adding this barrier seems to make it more robust

Get_count() should return the number of element
only when used on a Recv status. In this regtests
we were probing the value of a Isend status.

Likely openmpi sets it anyway as the number of
sent element, but this makes mpich2 fail the regtest.

I thus removed the check.

It seems in 865d16c9 I introduced a bug:
checks where reported to travis only when
building doc.

Fixed now

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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

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There was an error in passing masses from NAMD to PLUMED.

Found by Glen Hocky.

Fixes #162

to doxygen 1.8.7

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When MPI was requested and not found configure was erroneously
reporting that PLUMED was compiled with MPI support

\issue{123} to get #123 and a link at the github issue page

\branch{v2.1} to get v2.1 and a link at the github branch page

In 311f3e0b I forgot to rename
the link in Cambridge tutorial

I removed the sentence saying that 2.2 will crash.

We should likely make it fail on travis-ci so that
we remember to add the documentation, but I cannot
do it know as one regtest basic/rt44b in v2.2
would fail.

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This should show "master" instead of "2.3" in
online doc-master

Includes statistics of (style) warnings.
Can be used to see if the number of warnings decreases.

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closes #147

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closes #141

Before fix the master branch was installed
Now we explicitly ask for 1.69

Now $HOME/opt has the priority. This allows properly
overriding already installed programs.

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