This is an attempt to create more structure for LAMMPS-Tools.

The focus will be much more around the C++ lib and much less around Python.
All data types will be pure C++ and C++ only. Manipulation of them from
Python will only be by passing a pointer to said data structures around to
a C-like interface. This way, the library can also be extended to other
scripting languages and it allows me to program more in C++, in which I am
much more comfortable. It also enforces better thinking about which parts to
expose and which parts not to, which should lead to better encapsulation.



So, the basic design of the code will be like this:
            (exposed by)                 (called from)
C++ backend --------------> C interface  --------------> Scripting languages


Here are some examples of functionality in the three domains:

    C++ backend      |     C interface       |    Scripting languages
 --------------------+-----------------------+-------------------------
    neighborize      |  lt_neighborize(...)  |  Created by pybind11,
                     |                       |  cffi, whatever.

+==================  Building lammps-tools  ==================+
NOTE: If you simply want to _update_ a working lammps-tools to
a new version, this procedure is not necessary. Instead, follow
the steps described in Updating lammps-tools.

There are two ways right now of building lammps-tools:
CMake or plain old make. These instructions only really
work on Linux or Mac OS X, and probably BSD, not Windows.

There are some prerequisites:
 - Python 3 (>=3.4 seems to work)
 - CMake 2.8 or later (if you want to build using CMake)
 - A C++11-capable compiler (gcc >= 4.8 works)

In the guide shell commands are prefixed with a "$" and
should be run as is (without the "$" that is).

+==================  CMake                  ==================+
 0) This section requires that you have CMake installed.
 1) Follow these instructions to build the C++ library:
 1a) $ cd lammps-tools-v2
 1b) $ mkdir build
 1c) $ cmake ../
 
     Optional: Configure your build. If not necessary,
     continue with 2).
 1d) $ ccmake ../
 
     This opens a graphical interface in your terminal. In it,
     you can set some options. For older compilers, you'll want
     to disable USE_EXCEPTIONS and enable LEGACY_COMPILER.
 
     If the found compiler version is lower than 4.8, you need
     to change it to point to a higher version. Follow these steps:
     
 1d1) In ccmake, press t to enable "advanced options"
 1d2) Select CMAKE_CXX_COMPILER
 1d3) Press enter to edit. Change it to point to a modern C++
      compiler that fully supports C++11.
      Press Enter after you're done editting.
 1d4) Press c twice, and then g.
 1d5) Press q to leave ccmake.
 
 2) $ make
     This will build the library. You can speed it up by
     adding "-j<a number>" to build in parallel:
    $ make -j4
 3)  After building, copy the library to the lammps-tools-v2 dir.
     On Linux:
     $ cp liblammpstools.so ../
     On Mac OS X:
    $ cp liblammpstools.dylib ../
 
     Now we need to build the Python bindings.
 4) $ cd ../
 5) $ cd foreign_interfaces/python3/
 6) $ mkdir build
 7) $ cd build
 8) $ cmake ../

    CMake might fail to find a compiler that's recent enough.
    If so, follow these steps. Else, continue at 8e).
 8a) $ ccmake ../
 8b) Press t
 8c) Change "CMAKE_CXX_COMPILER" to a C++11-capable one.
     In particular, you need to pick one that supports pybind11
     (see https://github.com/pybind/pybind11, "Supported compilers").
 8d) Press c twice.
     
 8e) CMake might also fail to find Python, especially on clusters.
     If so, it will print a warning:
     "SEND_WARNING Could not automatically find Python! Set it "
     "yourself in advanced options!".
     If it finds Python3, continue at step 9). Else, follow these steps:
 8f) $ ccmake ../
 8g) Press t
 8f) Change PYTHON_INCLUDE_DIR to a Python 3 include directory
     (one that contains Python.h)
 8g) Change PYTHON_LIBRARY to a Python 3 library (libpython3.so (Linux)
     or libpython3.dylib (Mac OS X))
 8h) Press c twice. As of writing, CMAKE just repeats the aforementioned
     warning; ignore it. I need to fix that later. :$
 8i) Press g.
 
 9) $ make
10) $ cp *_.so ../lammpstools
11) Now you're all set. lammps-tools-v2/foreign_interfaces/python3 now
    contains a functional Python package called "lammpstools". You can
    test using it bu running Python3 and importing the module. Make sure
    that you use the same interpreter version as what you compiled against.
    That is, if in step 8 you compiled against libpython3.5m.so, your
    Python interpreter version needs to be 3.5 too.

12) $ cd ../
13) $ python3 -c "import lammpstools"
    If this command executes without errors, you can definitely use
    lammpstools with your interpreter. To be able to import it from
    anywhere, just make sure the module is in your PYTHONPATH. On Linux,
    if you use bash, this does the trick:
    $ echo 'export PYTHONPATH=$PYTHONPATH":'$( pwd )'"' >> ~/.bashrc
    On Mac OS X, this works:
    $ echo 'export PYTHONPATH=$PYTHONPATH":'$( pwd )'"' >> ~/.bash_profile

    Alternatively, you can copy lammpstools to a location that is already
    in the python path. This is more nice for administrators. Replace
    "<some dir that is in PYTHONPATH>" with a dir that is in PYTHONPATH:
    $ cp -r lammpstools <some dir that is in PYTHONPATH>
    
14) Now you're all set. You can just use "import lammpstools"
    in any python3 script and it should work.

+==================  make                   ==================+
 1) If you want to use GNU make, you probably already know what
    you're doing and you don't need instructions. :)


+==================  Updating lammps-tools  ==================+
If you already have a working instance of lammps-tools and simply
want to update (to get the latest features), follow these steps:

 1) Go to the lammps-tools-v2 dir.
 2) $ git pull
 3) $ cd build
 4) $ make
 5) On Linux:    $ cp liblammpstools.so ../
    On Mac OS X: $ cp liblammpstools.dylib ../
 6) cd ../
 7) cd foreign_interfaces/python3/build
 8) make
 9) cp *_.so ../lammpstools

  Done.