Update copyright statements and change license to LGPL

* I have followed http://www.gnu.org/licenses/gpl-howto.html
* Copyright is asserted for 2012 (which is needed for the license to
  have any effect)
* Mostly that meant amending the previous statements, most of which
  had no legal force anyway (e.g. using "2001-2004" requires that
  you spell out that you really mean every year in between is a
  copyrightable year)
* Many files had no copyright on them; now they do
* Licensing is now LGPL v2.1 (or later). Unfortunately a CPack
  limitation means we have to use just one file for all our
  licensing statements. That's not great, but it will do.
* Previous copyright statements are intact
* External code used under license retains that license statement
  in the code
* Changes were made with a Perl script so this pain is
  not so bad next time
* The copyright comment no longer names a specific version,
  so that we don't spam the git log for no real purpose.
* Removed some remaining emacs editor lines, CVS tags and GROMACS
  acronym generator spam
* Some code areas are not yet relicensed, pending anticipated
  updates e.g. AdResS kernels
* Group kernels have been regenerated so that both the templates and
  the code all bear the copyright - this will continue to occur for
  new kernel sets
* No duplicate copyright statements on essentially unmodified
  GPU memtest code used under license
* No duplicate copyright statements on unmodified thread_mpi code
* Don't bother licensing cmake/*.c files
* Don't bother licensing anything in share subdirectory

The following things we will fix after 4.6-beta1

* TODO vectype_ops.cuh probably from CUDA SDK needs attribution
* TODO fix licensing statements for things we have stolen from CMake
* TODO fix things under admin, scripts

Change-Id: I1c507b3feb9ec97d02c87d73cc66cfd5f7381c23
fixed issue with -multi and GPUs

Several GPU related parts of the code did not take the multsim
functionality and separate PME nodes into account.

Change-Id: I4f6471dfda3d14ed7ca33205c56849a27564c742
don't auto-set nvcc host compiler with cmake >2.8.9

Starting with CMake 2.8.10 the FindCUDA module set sets the nvcc host
compiler by default which clashes with our internal implementation of
the same feature. To support both pre-2.8.10 and later versions, this
change renames the CUDA_NVCC_HOST_COMPILER cache variable to
CUDA_HOST_COMPILER (used by CMake 2.8.10's FindCUDA) and avoids adding
the -ccbin option to the nvcc flags with CMake 2.8.10 and later.

Fixes #1051

Change-Id: I4d4048d520edb8655b88b6bae35f97df76a25910
Fixed labelling of g_hbond plots

Hydrogen-bond angle and distance distribution plots are now correctly
labelled.

This commit fixes #1052

Change-Id: Iadcc9c64b70de4a8c55b15d997b0c2ebd5a6db08
fixed segv in Verlet pair-search with trilinic DD

With the Verlet scheme and domain decomposition the bounding box
of the zone, used for the pair-search grid, could be calculated
incorrectly for certain triclinic boxes, causing array indices
to get out of bounds (usually causing a segv).
Fixes #1059

Change-Id: I5bb146baaec59271dd5e68b40c545ed29d061831
Keep FindCUDA quiet when it is not useful

If detection has been done and GPUs were not detected, a user who
didn't give orders about using GPUs should not need to worry about
anything with CUDA in the name. Otherwise, messages like
"CUDA_TOOLKIT_ROOT_DIR not found or specified" are emitted
by FindCUDA as warnings, and require user interaction when
using ccmake.

Change-Id: If31603a4bdfd72ca5ed4f0313f708b3efe778a74
fixed incorrect virial with virtual sites and OpenMP

The virial was incorrect with more than 1 OpenMP thread
and virtual sites crossing a box boundary.
Fixes #1060

Change-Id: Ib659f6eb7719f4808b37e828b96526587f8a0e69
Re-apply -dev version name between beta 1 and beta 2

We'll still have to strip it on and off for the release tarballs.

Change-Id: Ib71d0c593f4d16e4fee0e7ec012b8cc2f0099b65
Remove TEST_TMPI_ATOMICS_ONLY

Not needed anymore since aaf38d0b8683c510a5

Change-Id: Icce5578e7b1bd64a5dcfef1e2e38358ce5d9707c
Merge "fixed incorrect virial with virtual sites and OpenMP" into release-4-6
Merge "Fixed labelling of g_hbond plots" into release-4-6
Merge "fixed segv in Verlet pair-search with trilinic DD" into release-4-6
Merge "Re-apply -dev version name between beta 1 and beta 2" into release-4-6
Merge "Remove TEST_TMPI_ATOMICS_ONLY" into release-4-6
Merge "Keep FindCUDA quiet when it is not useful" into release-4-6
Merge "don't auto-set nvcc host compiler with cmake >2.8.9" into release-4-6
first step toward moving OpenMM support to contrib

Although this is a sloppy and incomplete solution, it's important that
for 4.6-beta1 the user at notices that OpenMM acceleration is not first
class citizen when it comes to support.

Change-Id: I494f3379865de4931af1eef8cbf09a63dba72648
fixed obsolete gmx_fatal in OpenMM build

Change-Id: I29686a897e1e38b2cc98165ba6c9521d3e29d0c6
don't warn during configuring if no GPUs were found

This change avoids issuing the post-configure GPU acceleration warning
if no GPUs were found in the build machine.

Change-Id: I63962c43ec9a8b9ee4f5ec2d1a19d4d819419ff7
Eliminate confusion from pkgconfig FFTW detection

If pkgconfig fails to find FFTW, it emits a CMake status messge,
but we do our own detection immediately afterwards. Seeing
a failure followed by a success can be confusing to users, so we
let them know we're not worried by pkg-config failing.

Change-Id: If270dd5d6fe10bc3a58a6fa56c9028cf61859d74