Essential dynamics output file now in .xvg format

No need to run a parser script on sam.edo anymore!

Change-Id: I37fcc7018482f31a25f5b6ba1bde7f22ccf0c31f
Hid nbnxn kernel names behind a lookup function

Keeps clang syntax checking in master branch quiet - otherwise
it complains about unused variables. See discussion in
Change-Id: I753f701d74b8d4533e74cede19712b030bf97ca6

Change-Id: Id73ef041d7d3c9443be4992dc18f28ac09f499e9
disable OpenMP with all OS X gcc 4.2-based compilers

Although gcc 4.2 should have OpenMP support, the gcc 4.2.1-based
compilers on Mac OS X (defaults in 10.6.x) all claim to support OpenMP,
but generates segfaulting code.

This change reworks the llvm-specific check and moves it out from the
C/CXX flag generation module.

This compiler is the default on many BSD os-es, but as no other gcc
4.2.x has been tested yet (to my knowledge), for now the limitation is
introduced only for the Mac OS X and gcc 4.2.x.

Refs #900

Change-Id: I1c2a27f6fc1162cf8999c65ff6173121109cfbad
Continuation of documentation for expanded ensemble.

With a few other corrections here and there.

Change-Id: Ic7ebefc8e959a50f2bba917fe90cbef4b44ab2fd
Merge "Continuation of documentation for expanded ensemble." into release-4-6
Merge "disable OpenMP with all OS X gcc 4.2-based compilers" into release-4-6
Merge "Hid nbnxn kernel names behind a lookup function" into release-4-6
Fix missing replacement/typo

Change-Id: Ia2b1c7a2aa222134c5d6847539d0f4287a3510a3
Remove debug statment

* left from I1c2a27f6fc1162cf8999c65ff6173121109cfbad

Change-Id: If520406444a810bf2810f68cf97a4a1bbf8141de