Release 4.5.6

- Updated the version to 4.5.6 in CMakeLists.txt, configure.ac
  and gromacs.7
- Regenerated man-pages and completions

Change-Id: I7692220dfe20248b4cdbdd1ed242d1d97f56fda5
Add fftpack to EXTRA_DIST

The new fftpack files added by 51c2f6c are only compiled if
fftpack is used. Thus "make dist" does not included those
by default.

Change-Id: Id51bba3c622a7087f35e74f7c499b066f095fd0d
fix invalid read in construct_vsites

* aj is not available in the F_VSITEN case hence cannot be read in
  the common part of the function

Change-Id: Ic98dfb91eb095aea933abc3dbfb4f5cc10bf4166
Plain text quotes.

And removed 5 gurgles and 2 bromacses - replaced the bromacses
by new and exciting ones.
Change-Id: Ibdad70d6ceb0caa52be351762704a677e9dddba8
Bump shared object version to 7

Almost certainly the ABI is binary incompatible for the 4.5.5 -> 4.5.6
transition, but we didn't think of handling the issue at the time.
So we can do so now.

Refs #1147

Change-Id: I15f978547d7fbcc9a72454067825c71c0ffb459a
Issue errors/warnings for ICC before 12.0.0

ICC 11.1 with SSE4.1 gives incorrect results, so CMake will
refuse to build with that minor version. Given that we
currently don't know anything specific and 11 is old, we
warn with any version older than 12.0.0. If more information
is available later, this warning can be made more specific.

Fixes #1126

Change-Id: I3c37844c69ce34769187f288c43cd8aef4086c53
Fix CMake namespace pollution

When gmxManageMPI finds MPI and CMake version is less than 2.8.10,
the variable file_cmd ends up in the non-advanced CMake namespace.
Made it advanced in those cases.

Change-Id: I79fd46e1b66d6c5ab008973e654092939eeae4dc
Made g_tune_pme work with 4.6 if user sets "-p" command line option

Added "-p" (performance statistics log file) to the list of files that
must not appear on the mdrun command line at launch time. (This would lead
mdrun to refuse to launch due to an unknown command line option.)

Change-Id: I268bbf6513709866b9a6a8d81c97706ccc832988
fixed GPU particle gridding performance issue

The scaling factor for the grid binning for the GPU pair search
was set incorrectly, which made the binning 50% slower.

Change-Id: I146592c37094a3d81a7ae50b3903fcc615e748d5
Merge release-4-5-patches into release-4-6

Avoided the 4.5.6 release patch by using
git merge -s ours 10b109beb3ffa95e37386d38140d2c0fd7769f20
git merge release-4-5-patches
tree=$(git log -1 HEAD --pretty=%T)
git reset --hard $(git cat-file commit HEAD | sed '1,/^$/d' | \
    git commit-tree $tree -p 2b05689 -p 8d6cc14)
Conflict resolution was straightforward, except that the vsite
code was somewhat reorganized in the meantime.

Conflicts:
        Makefile.am
        src/contrib/Makefile.am
        src/contrib/addquote.c
        src/gmxlib/copyrite.c
        src/mdlib/vsite.c

Change-Id: Ib90ac4e55fac308c433b15c344caf5ee41f0146c
fixed issues with FEP soft-core and cut-off's

Now the cut-off is applied to the PME mesh correction for perturbed
pairs with soft-core. Now the cut-off is applied to VdW with soft-core.
Fixes possible NaN in free energy kernel with r close to 0.
Replaced a confusing grompp warning with PME and soft-core by a note.
Removed an invalid grompp warning about soft-core and twin-range.
Fixes #1146

Change-Id: I79a06b20158df2bce575808b6e31e660163bd307
Bump shared object version to 8

libs are not compatible with the ones from Gromacs 4.5.x, which had so
version 6 through 4.5.6, and now so version 7 for 4.5.7.

Fixes #1147

Change-Id: If96fd044b00a99eb4ba8376ffa0a2ecbea37894a
added mdrun check for Verlet+perturbed atoms

Currently the Verlet scheme does not support perturbed atoms.
This will be implemented soon.

Change-Id: Id8656aa680b6581882f5371514cdbd85f429c418
fix imcompatibility with tpr vers<64 with free energy option

should fix to redmine #1156

Change-Id: I6e60f1efbb03bf460009b8bc59f80f2e0e15bf44
Uncrustified code changes since 4.6

The group kernel python scripts have changed slightly to emit
code that uncrustify won't want to change. Group kernel
generation and uncrustify are now mutual null operations.

Recent changes to the declarations in gmx_order in baa65b60
may have exposed a possible bug in uncrustify. Those declarations
have been simplified so that there will be no future issue from
that possible bug.

Refs #845

Change-Id: I33495d57ca37317cef4bf12707fd77d67309d292
fixed PME time print with -ntomp_pme != -ntomp

Fixes #1158

Change-Id: I9028e6309b8802125e91935e87d96b341ec30f77
Declaration-definition consistency nbxn_cuda_wait_gpu.

Changed float->real in nbnxn_cuda_wait_gpu() for consistency between
function declaration and function definition.  Added note that this is
only implemented for single-precision at the moment.  CMake will
complain if GMX_GPU and GMX_DOUBLE are both set.
Addresses Bug #1157.

Change-Id: Ide495cbaba6d120d91f106c6a87ca04e46a2f5a8
Merge "Uncrustified code changes since 4.6" into release-4-6
fix broken things in mkhtml

Change-Id: Ifb9aa694eddd4bffe457674265a2b17093182c50
Warn if X11 was not found and the user wanted it

Also, removed unused HAVE_X11 variable.

Change-Id: I581b2036f9de27a02c034230f2d1212b9814ffbb