Improve master-specific CMake behavior.

- Make GMX_BUILD_UNITTESTS independent of GMX_XML.  It now gets it
  default value based on whether libxml2 is found.  Also, if it is
  explicitly set, but libxml2 is not found, give a fatal error instead
  of silently disabling the tests.
- Mark GMX_XML as advanced and make it a no-op that it currently is
  (nothing in libgromacs actually depends on libxml2).
- Rename GMX_INTERNAL_BOOST to GMX_EXTERNAL_BOOST to match BLAS/LAPACK
  settings.  Set the default for it based on whether Boost is
  actually found.  Print the existing message on the first run if
  GMX_EXTERNAL_BOOST was not explicitly set.  Give a fatal error if
  boost is not found and GMX_EXTERNAL_BOOST=ON instead of silently
  changing to use the internal boost.
- Move installation rules etc. for boost towards the end of the
  CMakeLists.txt file to use INCL_INSTALL_DIR in them.

Now, cached values for these variables really describe what is going to
get build.  Also, explicit user choices are never overridden, but result
in fatal errors if they cannot be satisfied.

Change-Id: I5b3f93eecff2ccc4bf8d348392dd4ae30efd9f92
Fix bug in selection subexpression handling.

Did not work correctly if
1. a static expression was passed to a SPAR_ATOMVAL parameter,
2. other parameters to the same selection method were dynamic
   (so that the expression would not be completely eliminated during
   compilation), and
3. the evaluation group of the SEL_EXPRESSION element was dynamic
   (so that the SPAR_ATOMVAL expression could be evaluated for a
   different group during evaluation and compilation).
In this case, the static atom-valued parameter got evaluated during
compilation for the maximal evaluation group and replaced by a constant.
During evaluation, if the evaluation group was smaller, the values for
that expression were no longer correct.
See #1216 for what kinds of concrete selections this applies to.

Subexpression handling in the selections is starting to (again) get very
messy, but that is a topic for a larger-scale refactoring...

Fixes #1216.

Change-Id: Ic6b7f9b8df661a9c78d7862b981a07e65a7ebdbf
Fix another bug in selection subexpression handling.

In this case, it did not work correctly if a variable with a dynamic
value was used both
1. in a boolean expression such that its evaluation group was not known
   in advance, and
2. in a context where it was always evaluated for all atoms (either as
   a selection, or as a parameter to a selection method),
and additionally the latter context appeared later in the selection set.
The initialization of the SEL_CDATA_STATICEVAL flag has a dependency on
SEL_CDATA_FULLEVAL flag, and they were not initialized in the correct
sequence in the above case.

Fixes #1219.

Change-Id: Ic95d37a424c82c796806b3a5b39678e206c467a1
Updated source for Van der Waals radii.

Implemented new Van der Waals radii in atomprop. This may
have an effect on results from gmx sas or editconf and therefore
a message is printed to notify the users of this.
The genbox program is adapted to have an extra option to scale
the Van der Waals radii, in case it is difficult to add extra
atoms. The default value for this option is 0.57 which gives approximately
the same density as old genbox.

Change-Id: Ib5d86a920ae7732ee8a29505449e6d34e3d3980c
Merge "Fix bug in selection subexpression handling."
Merge "Fix another bug in selection subexpression handling."
Remove gmx_ana_index_t::name and unused code.

Remove the name field from gmx_ana_index_t, which was in most cases
NULL, and was a source of multiple ugly hacks in the selection code to
avoid leaking the memory allocated for the name.
Now that SelectionTreeElement has a proper std::string name member,
there is no need for this name field anywhere in the selection code
where the atom groups are handled as selection values.

Also remove unused code from indexutil.* (that would have required extra
effort to not break it).

Change-Id: I14698c17da3b479de4016a6188fcd235514b9e2a
Merge "Updated source for Van der Waals radii."
Merge "Improve master-specific CMake behavior."
Merge branch 'master' into alexandria

Conflicts:
	src/gromacs/gmxlib/atomprop.c

Change-Id: Id2409bab6eb59dba6cfe2dc7e0800185f02f0240