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Added flag to spins.conf for derivatives.cpp to compute Baroclinic Vorticity

See merge request !8

Fixed merge conflict in derivatives.cpp

Master

See merge request !6

The derivatives case file now computes Q and R--invariants of grad(u,v,w) that are useful for vortex identification

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