[makedoc]

[makedoc]

This fixes an issue on periodicity of values.

Now all the values are brought within their periodic boundaries.

I do it since an error in the last digit was making the
*next* commit fail. I first change the regtest to make it clear
that it is not changing

travis is very picky and does not understand "allow_failure"
if there is a wrong number of spaces

cppcheck is installed from its github when needed

Notice that the travis test doing cppcheck also does a normal g++ check.
I did to avoid too many if's in the travis script, but should be fixed perhaps
so that the last travis test only does cppcheck

I set this test as "allowed_failures", so that is just gives a warning now

I invoke cppcheck from an external script that makes the reporting better.

In particular, I show "fatal" errors at the end, where "fatal" means
all reported issues with the exclusion of "style" issues and issues
in molfile sourcecode.

Before this fix, the PLUMED_KERNEL env var was erroneously not
containing the LIBSUFFIX value.

This fix is relevant only if one use at the same time PLUMED_LIBSUFFIX
*and* loads the module file, which is unlikely.

gromacs-5.1.0 beta patch

[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