gmxpreprocess: clean up -Wunused-parameter warnings

Clean up (most) of unused params

Change-Id: I1805a829682baf54047390442bfcfa2a95cd0ee1
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Added citation to free volume paper.

Change-Id: Idcc8d29813e13f259048e7ad6cc1f72b70cd7229
Support for storing multipoint analysis data.

Main changes:
- The storage frames now store a vector of "point set info" objects,
  which partition the vector of values into point sets, and annotate
  those sets with extra information (currently, the index of the first
  column).
- The implementation of the frame access wrappers in dataframe.* are
  adapted similarly, and methods are added to allow access to multiple
  point sets within a single frame.
- Added tests for multipoint storage.
- Other changes are adapting to these interface changes.

Still doesn't work perfectly; full support for addColumnModule()
requires reworking the logic in dataproxy.cpp.

Part of #869.

Change-Id: I21141bad83b3f2bb72ece9146aaec02792e6cd0e
gmxlib: clean up -Wunused-parameter warnings

Clean up (most) of unused params

Change-Id: Ibbe8d775ca1c37338f968d124d773808a1784eae
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
linearalgebra and fft: clean up -Wunused-parameter warnings

Clean up (most) of unused params

Change-Id: Iaad4b2d1a98584d6d72cdd1ecf43b788d9753715
Signed-off-by: Alexey Shvetsov <alexxy@omrb.pnpi.spb.ru>
Extract Doxygen comments within #ifdef __cplusplus.

Also add documentation for some undocumented thread_mpi members exposed
by this.

Change-Id: I93ff0770d4032b92dc829257f773c11a93d78caa
Uniform and less verbose startup for all binaries.

Now all binaries call gmx::ProgramInfo::init() as more or less the first
thing.  Removed set_program_name() as unnecessary, since the above call
does all that.  Make CommandLineModuleManager responsible of also
printing any common startup header, and add a method to suppress this
stderr output in unit tests.

Replace CopyRight() with a less verbose method and move the
responsibility of calling it to parse_common_args().
Added a PCA_STANDALONE flag for parse_common_args() to know when to do
this (can be removed once all programs are part of the wrapper binary).

Left the CopyRight() function still there, in case we want to add a
-license command-line option or similar to print that information.
Currently, it is not called from anywhere.  Removed GMX_NO_CREDITS and
some other unnecessary code from CopyRight().

Most stuff in contrib is broken by this.  There may be more changes
coming to the initialization sequence, and it will be simple to adapt
those programs that people want to get working again, but it is not
worth doing it more than once.

Part of #1209.

Change-Id: I5403dd259ab5f314cce3283aac275a6c26d4818d
Pre-emptively fix some C++ warnings.

Moved sepdvdlformat from force.h into a source file to avoid warnings
about an unused variable.  These appeared as soon as a C++ source file
included force.h.  As an additional benefit, makes printing this
information more typesafe; this is how #1294 was found.

Change-Id: Id856fbe193d9b4a74ecfb49cba9eab03bad0a7ba