That occurence of rDock was wrongly generalized to |Dock| (so it can be
rDock or RxDock depending on the value of the replacement text).

Thanks to Sergio Ruiz Carmona <[email protected]> for
spotting this mistake and reporting it.

Also changed one wrong occurence of rDock in the User guide to |Dock|,
where we link to download links for RxDock.

This yields more performance; in multiple tests I measured about
10-12% speedup using rbcavity.

The matrices used are self adjoint so the SelfAdjointEigenSolver
performs better than the generalized one.

In the test performed by the command:

rbdock -r 1YET_test.prm -i 1YET_c.sd -p dock.prm -n 2 -s 48151623 -o
1YET_test_out

the SelfAdjointEigenSolver saved about 8% of total execution time
(measured with the function profiler).

- default constructors
- std::string references
- std::move in constructors
- auto& and range-based for loops

Some systems and compilers might not support OpenMP so made OpenMP a
non-mandatory dependency.

Partial credit goes to Patrik Nikolić <[email protected]> for
the composition of some figures.

- Initialized base class RbtContext in the copy constructor of the
  derived class RbtStringContext
- [-Wdeprecated-copy] explicitely declared operator=(const &) for
  RbtCell and RbtVble

Updated logos and documentation accordingly. Versioning changes:
- Removed EXEVERSION which was wrong anyway since we haven't used
  CVS $Id$ values since forking.
- Removed IDS_BUILD which we didn't use and it ain't going to work in
  the future if we want to support reproducible builds.
- Restarted versioning from 0.1.0 since the plan is to use semantic
  versioning from now on. Removed separate include/VERSION and
  integrated into RbtResources.h which will eventually be generated
  by Meson at build time.

Cleaned up inconsistent use of tabs and spaces and replaced old style
string formatting (%) with new style (.format()).

Open Babel 3 puts pybabel module inside openbabel, so import has been
changed to try that first and fall back to 2.x style import if the first
import fails.

In addition, ran perltidy on the scripts and removed a duplicate of the
header in sdmodify.

To make the change less distruptive, RowMajor order is still used, but
the array indexing is now from 0 instead of 1, which simplifies the
code quite a bit. Built-in Eigen functions are used where possible.

Nelder-Mead implementation used previously was previously built on top
of TNT. Since the usage of TNT was replaced by Eigen, it's reasonable
to use Eigen for Nelder-Mead as well. Thanks for the implementation
guidance go to Matthieu Brucher: http://blog.audio-tk.com/

Partial credit goes to Dominik Kinkela <[email protected]> for
the experimentation regarding the implementation approach.

Reduced CSS min-width from 450px to 240px.

- missing include guards
- new without delete
- declared variable hides function parameter
- unsigned comparison with zero
- dangerous/obsolete function asctime replaced with std::put_time

Fixed wrong (missing or extra) executable permission on data files.

Removed support in rbdock command for -t option without -C so -t now
has a unique meaning. Previous meaning of -t without -C (filter file
name) is provided via the newly added -f option. Now there is no need
to distinguish during runtime which variant of -t has been requested,
which simplifies the code and makes it more robust.

EIGEN_DONT_VECTORIZE define is required with the PGI C++ compiler, as
otherwise the code doesn't compile due to a multiply defined function.

More details are on the PGI User Forums topic "Error compiling with
Eigen library": https://www.pgroup.com/userforum/viewtopic.php?t=6690

Normally this should only be used for MSVC as MinGW provides dirent.h,
but it turns out that the provided dirent.h is not sufficient for our
usage.

PCG fails to build on Solaris and Windows/MSVC. Use instead whatever the
compiler and the standard library provide as the default C++11 RNG.

Issues on GitHub:
- Solaris: https://github.com/imneme/pcg-cpp/issues/42
- Windows/MSVC: https://github.com/imneme/pcg-cpp/issues/11

PCG (pcg-random.org) is a family of simple fast space-efficient
statistically good algorithms for random number generation. Unlike many
general-purpose RNGs, they are also hard to predict.

The C++ implementation follows the conventions of other C++11-style
generators (WG21 N3551) and is available under the Apache License
version 2.0.

Changed 1E-10 to 1E-7, i.e. reduced by three orders of magnitude. 1E-4
is used by default so 1E-7 is still finer than that.

Unlike MSVC, GCC and Clang pass the tests with threshold down to 1E-14.

MSVC doesn't export static member variables as symbols. Replaced access
to these variables with getters returning a (const) reference.

Introduced a macro for __declspec(dllexport) and added where necessary.