=== Science ===
The directory Science/ now contains files corresponding to
the various functions in the now-removed Science.cpp.

Filenames correspond directly with the function name, and each
file contains only one functions, with a few notable exceptions.
 - Science/get_quads.cpp contains get_quads_x, get_quads_y, and get_quads_z
 - Science/compute_background_PE contains the helper function
compare_pairs

The global variables _quadw_x, _quadw_y, and _quadw_z are declared as
extern in Science.hpp and declared in Science/compute_quadweights.cpp

=== Makefile ===
The Makefile has been modified accordingly. It now automatically detects
all Science/*.cpp files and includes them in the compile recipe.

The Makefile has also been tidied up a little bit by defining a variable
SPINS_BASE which points to the core files.

The energy transfer rate from internal energy to BPE is generalized
to handle both mapped, and unmapped cases. What had been there
was in fact correct for both, though it wasn't realized at first.

Archived old wave_reader cases.

Minor fixes in other case files.

The stress along the bottom and top surfaces are calculated
and written to a file (stresses_(top/bottom).txt) using the function
stresses_top and stresses_bottom in BaseCase. These functions are
especially useful with mapped cases.

The dimensional rho option should not be after the mapping options
since the mapping options will need to be specified for an
unmapped dimensional density case. This now makes the optional
argument ordering more logical.

This is the last energy conversion term to get a complete
energy budget.

The BPE calculation had assumed that the density field was
non-dimensionalized as the density anomaly. An optional argument
allows the user to set the density field as dimensional.

The mapping affects how to spead voxels out at a given depth.
A sorted hill makes loops easier, and thus the calculation of the
surface area for a given voxel that intersect the hill.

The background Potential Energy (BPE) is calculated in
compute_Background_PE in Science.cpp. The APE can
be calculated afterwards from the BPE and PE from the
diagnostic file.

A new case file, derivatives.cpp, gives a means to compute
derivatives of any field or to compute vorticity components.
The vorticity calculation in Science is completely re-written
so-as to also work for mapped grids.

The derivatives file is built to compute secondary variables
after a run has already been completed. This uses spins' built-in
derivative toolkit allowing multiple variables to be calculated
in parallel. A derivative field (one that is the derivative of
another) is denoted by an underscore followed by the direction
the derivative was taken in (ie. u_x is the x derivative of u).

A new case file, derivatives.cpp, gives a means to compute
derivatives of any field or to compute vorticity components.
The vorticity calculation in Science is completely re-written
so-as to also work for mapped grids.

The derivatives file is built to compute secondary variables
after a run has already been completed. This uses spins' built-in
derivative toolkit allowing multiple variables to be calculated
in parallel. A derivative field (one that is the derivative of
another) is denoted by an underscore followed by the direction
the derivative was taken in (ie. u_x is the x derivative of u).

- Added 1D and 2D outputs
- Added parallel writing and reading

From a version of this code that was floating around, added read_2d_restart
to Science.[ch]pp; this reads a 2D array from disk that was previously
written by a SPINS job and extends it along the y-dimension to fill the
given array; this is useful for extending 2D runs to 3D.

This is the initial commit of SPINS to a git repository, coming from
an essentially unmanaged environment.  While this is a *complete*
archive, this is probably not the most useful form for development
going forward.  Notably, the future management should be:

1) Pare down the case files

2) Establish branches for individual users.  Not as a long-term goal,
   but instead to keep user-specific case files from lingering in
   the main repository long after their use is obsolete.

2b) Establish semipermanent branches for typical users.  A release
   branch should include the basic documentation cases, a benchmark
   case should include benchmarking cases, and there are probably
   others that aren't coming to mind now.

3) Add helpful MATLAB processing scripts to the repository.  Too
   much of that is ad-hoc now, completely unmanaged.

4) For papers/etc, establish tagged versions.