Version bumps before release

Change-Id: I5b5ea233c47ce95474dae3b0f71a4ae6ae704f6c
Version bump after 4.6.5 release

Change-Id: I1d1c1ee28d585b6cf4431f9f1ec1a334f68ae6e3
Don't create symlinks in the build tree

This requires an update to the regression tests and/or Jenkins.
Either the regression tests must be run against installed code, or they
must be modified to not depend on the symlinks.  But that would be for
the better, as the present approach (that is removed here) is a hack
that doesn't always work, and since we want to get rid of the symlinks
in the long run, it doesn't make sense to try to make the symlinking
more elaborate.

Change-Id: I90859f1a8c15d8ac3090e31f522aae2af7ba4a67
Avoid build error if CFLAGS contain quotes

Because the BUILD_CFLAGS wasn't escape copyrite.cpp would
fail to compile if CFLAGS contained quotes.

Change-Id: I347512a6574ebbcd0f29d1bc4cd26423f3d323ee
Moved OpenMP detection to separate file.

This cleans up the main CMakeLists.txt file a bit and
removes manual line breaking from the OpenMP warning
message. It also emphasizes the different parts
(compiler detection, finding package, and final setup)
that are part of the OpenMP detection in Gromacs.

Change-Id: Id13e555d8dac1b5e8bb9c07111a4546a3b438a55
Moved compiler problem detection into separate module

This makes the main CMakeLists.txt slightly more readable.

Change-Id: Ibbae29ef89578587a4d103b5176b7bf0eda2d82b
Moved FFT library processing to separate module

Helps make the main CMakeLists.txt more readable.

Change-Id: Ia846863edb4471c9c85480d82b5c5cce4225b074
Moved shared/static library detection to separate module

Helps make the main CMakeLists.txt more readable.

Change-Id: Iaf1c3734ceeaf36a532be424c7429931534844d5
Added a bunch of quotes from the 2013 Nobel lectures

And our string-reading routines have been updated to use
our standard length STRLEN, which is currently 1024 chars.

Change-Id: Id3e2c07774ee98cf6d4e58534c5f87821516d5a8
Clean up old command line parsing

- Move pargs.c to C++ compilation to enable some of the below changes.
- Move *scan() routines from statutil.h/.cpp into pargs.cpp and make
  them static, as this is the only place where they were used.
- Remove vscan() declaration in statutil.h, as the function was not
  defined nor used anywhere.
- Move nenum() declaration from statutil.h to readinp.h, and the
  implementation from statutil.cpp to pargs.cpp.
- Remove unused pdesc() in statutil.cpp.

Clarifies the code somewhat, and removes unnecessary declarations from
headers.

Change-Id: I0b70f3622c8bea41bf88b677cbe202143a3e60c9
Fix non-critical typo in #ifdef GMX_OMPEN_MP

Added #include to make it work.

Change-Id: Icea244c4fb63aee6ae67a29370d08177a66129a8
re-add Carsten & me to the copyrite

Change-Id: Ie7dd5467346f55c4c1830547b3a08473d7e66c64
Clean up trajectory time control

- Create a separate header for the routines defined in tcontrol.c.
  Move declarations there from statutil.h.
- Move the implementation into fileio, since that is mostly where it is
  used.

Change-Id: I59579f0bddd73d182d04c7ab160a0b547f66ebe2
Move Program() and ShortProgram() into copyrite.h

Part of effort to split up statutil.* into their component parts.
The most natural place could be utility/programinfo.h, but that would
require extra effort.  With some C++ conversion, we could also
completely get rid of at least Program(), so did not want to go through
that now.  copyrite.h already has GromacsVersion(), so this somehow
fits.

Change-Id: If82e0e924025ab782f090cb5b0542a6d01689d9e
More Nobel quotes and others

Change-Id: Ice6543f2241a7b8cc03a1e650748110135d49f4d
Move pargs.cpp into src/gromacs/commandline/

- Move the source file and clean it up a bit.
- Move the declarations from readinp.h into a separate (new) header,
  named the same as the source file.

Change-Id: If1775a7387a164bed4fdb2a1d67457d8068f5c6a
Move parse_common_args() into commandline/pargs.*

- Remove statutil.* as empty after the move.
- Remove unnecessary inclusions of statutil.h.
- Replace remaining inclusions with either pargs.h, or one of the
  headers previously included by statutil.h.
- Make get_pargs() internal to pargs.cpp, as it is no longer called from
  outside the file.

Change-Id: Ie171eff303596ae3eb254d505d8c8b84dff1f84f
Replace gmx_large_int_t with gmx_int64_t

Most changes are only the rename:
gmx_large_int_t -> gmx_int64_t
gmx_large_int_fmt -> GMX_PRId64 (or GMX_SCNd64)
gmx_large_int_pfmt -> "%"GMX_PRId64 (with space for cpp)
SIZEOF_GMX_LARGE_INT -> 8
GMX_LARGE_INT_MAX -> GMX_INT64_MAX
GMX_MPI_LARGE_INT -> MPI_INT64_T
str_to_large_int_t -> str_to_int64_t
get_egmx_large_int -> get_eint64

Exceptions:
simple.h: Adding of new type
xdrd.c: Remove code for SIZEOF_GMX_LARGE_INT!=8
thread_mpi: Add MPI_INT64_T type
scanner.*: Insert #include for simple.h to fix macro issues

Change-Id: I99abbec0ecafb2580ddba89677a110c137e9abd6
Fixed compilation issue due to gcc4.8

by turning off warnings.

Change-Id: Ice3dd8dec8cb9dc590fb293c1face3ed603f7abb
Fixed essential dynamics (ED) continuation from .cpt for reference=average

ED runs where the reference and average structure indices are the same can
crash when continued from checkpoint. For these cases (where reference =
average atom indices) obviously the set of atomic positions for the reference
and average structures is always identical. Therefore, only one of the two
structures is stored (which is the average structure edi->sav). When reading
the old values of these structures from the checkpoint file, edi->sav.x_old
therefore needs to be copied both to xstart and xfit in init_edsam().

Change-Id: Ieb1f029f4a927999dfb4579ee7c3bebe15071dc8