[makedoc]

This reverts commit b148b715.

This should go with a94b94b2

[makedoc]

It seems the lapack routine I took from gromacs are not threadsafe.
Indeed, routines slasq5 and dlasq5 contained static variables.
I removed all of them and everything seems to still work correctly.
This seems to solve the problem that @gtribello
found in his no-buffer branch.

an INCLUDE, i cannot figure out if there was a reason for that

Now all png needed for the manual are copied to html dir

[makedoc]

I put no box info in the first frame so as to check this:
f4ca4c5d.

There was an extra copy of the box in ActionAtomistic,
namely ActionAtomistic::box and ActionAtomistic::pbc.

This means that one should take care of both copies when changing it,
which is error prone.

I eliminated ActionAtomistic::box

ActionWithVirtualAtoms should clean up the force on the virtual
atom when applied. Otherwise, actions computing the force on the
center of mass (such as FIT_TO_TEMPLATE) could compute it
wrongly when virtual atoms are defined.

I also modified a regtest so that it checks what happen when
using COM after FIT_TO_TEMPLATE

[makedoc]

- updated patch to include api version
- updated patch to inclide virial fix
- updated patch to gromacs 4.5.7

hopefully will avoid some mail to the mailing list

I implemented a framework to provide the virial corrections for
virtual atoms that are non-linear functions

I added the possibility to dump the 9 components of the virial
from the driver.

This is not strictly necessary since virial is
set anyway (and not accumulated), but I added
it for consistency.

If you had your atoms distributed among the domains such that one
node had on all the Atoms there could be a problem in running plumed.
This change fixes this problem.  Also deleted rogue check in
AdjacencyMatrixAction

[makedoc]

I changed a few things:
1. instead of checking with "--enable-debug" and "--enable-debug --enable-debug-glibcxx"
  I always use both.
2. I check with debug flags and serial compiler (before it was only debug+MPI)
3. I changed the order so that runs with manual is the first and runs
  with debug options are also made earlier. This is convenient since they
  take more time

This allows reading crd files without linking external plugins

(goes with 32c10c65)

ReferenceConfiguration::getReferencePositions() was hidden by
ReferenceAtoms::getReferencePositions()
since the former was const. I changed the former to non const.

@gtribello might want to check this