Merge "SelectionCollection::Impl is now properly private."
Merge "Selection::_sel is now properly private."
Documented the function of g_cluster -cl -noav

A definition was needed for the center of a cluster.

Change-Id: Id1c6d2f229feb27b7981c2d616e78e510d215a9a
Added CMake Toolchain file for BlueGene/P

Change-Id: Iff9b5fe3cccc4d18fc252856a1b50ee64630b54a
Introduced fatal error in grompp for incorrect use of settle and charge groups.

Change-Id: I02dfe3f3454a6fc329d9b5ecb2fd4b544c8d2cd1
Merge "Documented the function of g_cluster -cl -noav" into release-4-5-patches
Merge release-4-6 into master

Conflicts:
	cmake/gmxCFlags.cmake
	src/gromacs/gmxlib/tpxio.c
	src/gromacs/legacyheaders/gmx_wallcycle.h
	src/gromacs/mdlib/gmx_wallcycle.c
	src/gromacs/mdlib/sim_util.c
	src/kernel/CMakeLists.txt
	src/programs/mdrun/runner.c
	src/tools/gmx_tune_pme.c

Moved rotation files to correct folder for 5.0
Fixed double inclusion of openmm in runner.c

Change-Id: I115e47715a4d2980d196e1c75bfbbb595b1201d0
Removed old gmx_ana_selection_t.

Moved variables previously held there to member variables of the
Selection class.  Added private member functions to the Selection class
to remove direct member variable access from SelectionCompiler and
SelectionEvaluator.  Makes it easier to restructure the Selection
implementation since access to the member variables is now (mostly)
limited to selection.cpp.

Part of issue #827.

Change-Id: I60b302409afc1f9535ddd7423a8c2f4f3799f72e
Print context on reference data check failure.

Previously, the error message given for a mismatch against test
reference data would only print out the values, but no context, which
often makes it impossible to know what went wrong without a debugger.
Now, the output should be at least a bit more useful, in most cases
uniquely identifying the reference data element that failed.

Change-Id: Iea39529e629ea01fc4ee2b9286de71f73e4452c8
Fixes that failed Unit Tests were ignored (#859)

Change-Id: Icbef72747c0cad9ecc89c4acb2a0676e744ec8b2
Made use of VMD plugins more robust

Attempt to use VMD trajectory-reading plugins only if plugin
loading functionality exists and shared libraries are being used
(else dlopen can be unreliable).

Also, for helping to find those plugins, the user can supply the plug-in
path in a CMake cache variable. If not, the code can now fall back
on the run-time value of the environment variable VMDDIR, or its
value at configuration time. Previously only an explicit run-time
environment variable or a hard-coded path was available on non-Windows
platforms.

Also printed diagnostic text when GROMACS cannot tell if the
trajectory being read by a plug-in might have atom velocities.

Fixes #598

Change-Id: I44267e115267772dae2c1d754895f8ff25c98a6a
Check for VMD plugins that they are at least abi-version 10

All plugins with VMD 1.8 are abi-version 10. Plugin support is
untested for older versions.

Change-Id: I98fe11313d7115d476e44bff0bc729c7380c52f0
Merge "Removed old gmx_ana_selection_t."
Fixed use of _snprintf_s with MSVC

Change-Id: I807ef17e8b4eb07861600c6a1d9d03f330f17218
Fixed MSVC compiling with plug-in support

Fixes #598

Change-Id: I8fe274a83c4965466f1241d2237ca3e77b93b038
Fixed use of isfinite and _isfinite

Implemented proper CMake tests for the above functionality.
Catered for MSVC idiosyncratic _finite() function. Removed
erroneous use of HAS_ISFINITE and HAS__ISFINITE.
Encapsulated the use of preprocessor directives into the new
gmx_isfinite() function so the programmer doesn't need to
know about the foregoing mess.

The previous versions resulted in unreachable code.

Change-Id: I7471388ed8f402c3f8b664e7846465de4b85f578
Adds AdResS feature to gromacs

This is actually a rebase of the following commits:
* backport adress to 4.5, was ported from adress branch, which is based on the master
* update init_forcerec in gmx_membed.c due to adress
* energy terms in AdreS only caclulated for meaningful properties.
* adress variables only printed if adress is used
* grompp checks to prevent adress being used with lr coulomb or pressure coupling
* Windows/C90 fixes
* put inputrec variables into adress struct
* increases tpx_version from 74 to 75 (as enforced rotation was 74)
* rebase to recent 4.6 branch
* bAdress to false for tpx < 75 (disabled by default)

Change-Id: Ica1d121f8edb9086ac2d5d456b1037a3d57a24e4
Merge branch 'release-4-6' (incl. AdResS Patch)

Conflicts:
	CMakeLists.txt
	src/gmxlib/CMakeLists.txt
	src/kernel/CMakeLists.txt

Change-Id: I9760ea1165deb8ee5d38e476a0a24689621af39f
Removing outdated vsite comment

Vsite parameters were replace by Berk in commit 14bc4ad9 by
calculated parameters. Since then the comment was outdated.

Change-Id: I6ddacfbdcf40e11db9d2d3091d9c34f4872816bc
Merge "Fixed MSVC compiling with plug-in support" into release-4-6