Added declarations for two functions: one that computes Q (the second invariant of grad(u,v,w)), and one that computes the R (the third invariant of grad(u,v,w)).

This had been mistakenly set to 9.81 m/s^2, but a better default
option is for the tracer to be passive.

Previously, wave_reader computed the hill height as a fixed

  zgrid(:,1,1) - MinZ // matlab notation

which implicitly assumes that z increases along the third index.  If
that assumption is violated, the BPE calculation breaks (in ways that
can cause assertion failures based on roundoff error, at that).

Fixing the calculation as min(zgrid(i,1,:)) at initialization time
alleviates this problem.

Previously, wave_reader locked 'FULL' (3D) input behind enabling
restart.  This restriction was unnecessary, and doing so in fact made
the specification of u/v/w/rho filenames useless.

Deleting this check allows proper read-in of FULL datatypes, without
faking a restart.  The only functional difference is that if
perturbations are also enabled, they will be applied on top of the 3D
data read.  This seems to be desirable, since it makes the application
of the config-file settings more straightforward.

Based on experience with a poorly-converging, steep hill case, the
number of inner iterations in GMRES is increased to 40, and the number
of outer iterations drops to 2.

Please pay attention to GMRES warnings and report cases where things
don't work well, there's probably an optimal parameter range (or else we
could make the parameters a runtime config option).

The quadrature weights were found to be incorrect for mapped grids
because they were adjusted using the topography which was not
scaled properly. The topography needed to be adjusted to be relative
of the 'minimum z-value'. This is in quation marks because it is
not necessarily the absolute minimum, but rather the reference
minimum.
This shift also fixed the BPE calculation to have the same reference
as the PE calculation.

The previous "fix" swapped rho and tracer.

Update to version 2.0.4

Vortex stretching is one of the dominant terms in both the
vorticity equation and enstrophy equation. They also help in
understanding the vortex dynamics and how energy at large scales
cascades into small scales.

The three components of vortex stretching (omega dot grad) u
and the enstrophy stretching production (omega_i omega_j S_ij)
are now included and can be computed with the derivatives
case file. Files for vortex stretching terms are called
vort-stretch<dim> where <dim> is one of x,y,z. The enstrophy
stretching production file is called enst-stretch.

As these quantities are the product of velocity gradients, care
must be made to ensure adequate resolution is present.

Update version to 2.0.3

Update version to 2.0.2

Updated version to 2.0.1

The GitLab interface also supports hosting a contribution guide.
This guide is fairly basic, but outlines three main points
1. Talk with Chris Subich before merging changes
2. How to submit a merge request via GitLab
3. Version number etiquette

GiLab (and other git servers) include the main README as the front page
of the repository. This commit initializes the README with basic
information including a link to the thesis, paper, and relevant page on
the fluids wiki.

Running './casefile.x --version' prints the SPINS version with which
the executable was compiled.

The SPINS version is now the first thing printed in a simulation.
Also fixed typo in writing the grid in BaseCase.cpp

The file VERSION now records the MAJOR_VERSION, MINOR_VERSION,
and PATCH_VERSION.
To update the version number, the user only needs to modify the
appropriate lines in VERSION.

Makefile has been updated to automatically pass the version
information through compiler flags.

BaseCase.cpp has been updated to add a print statement into the
initialization function. By default, every casefile that uses
BaseCase will now print the SPINS version with which is was compiled.
This should help avoid issues with mis-matched versions.

It will appear in the output as:
SPINS Version 1.0.1

The starting version is set to 2.0.0

StackOverflow has a nice summary of when to change which version number
(https://stackoverflow.com/questions/3826580/what-rules-does-software-version-numbering-follow)
 - Major version numbers change whenever there is some significant change
being introduced. For example, a large or potentially
backward-incompatible change to a software package.
 - Minor version numbers change when a new, minor feature is introduced or
when a set of smaller features is rolled out.
 - Patch numbers change when a new build of the software is released to
customers. This is normally for small bug-fixes or the like.

Fix cfl calculation for mapped grids

Closes #6

See merge request !5

Refactor Science.cpp to split functions into separate files.

See merge request !1

=== 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.

Combined the mapped and unmapped cases for this into a single
case file.

With the retirement of belize, which formerly hosted a fixed
copy of the dependency libraries, make_deps.sh would no
longer download and build said libraries.

These libraries are now instead hosted in a dedicated
repository at UWGit, so make_deps.sh has been changed to
clone this repository.

The order of the input arguments for compute_vort_x,y,z was changed
some time over the last year, but this was not accounted for in
the calculation for enstrophy density.

This case has uncovered that the BPE calculation returns
incorrect values when a Chebyshev grid is used on a field scale.
The BPE calculation uses the quadrature weights as the volumes
of each cell. This is true when the grid is regular, but incorrect
for Chebyshev grids.

To first approximation the Cheb quadrature weights are close to
the volumes of the cells. This leads to the BPE calculation
being accurate to 8 significant figures. 8 sig figs is not enough
on fields scales since the magnitude of the PE can be very, very
large. The difference of the BPE from the PE can thus be smaller
than these 8 sig figs.

Some simulations have a long clock time per step, but have a short
write to disk time. If only the short write to disk time is
accounted for in the check_and_dump command then insufficient
time may be allocated for the dump to disk. Both are now accounted
for.

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 full xgrid and ygrid are unnecessary since x and y only
depend on a single variable (or index - ii for x, and jj for y).
The variables xx and yy can be used instead of xgrid and ygrid,
respectively. Creating the full grids for these fields is a
waste of memory.