Add QSPCount method to Science

See merge request !12

On belize2, the new blitz version failed to build because of an error
related to autotools.  Adding 'autoreconf -vif' to the build magic
causes the missing files to be regenerated, resulting in a successful
build of blitz.

Resolved merge conflicts in Science.hpp, derivatves.cpp, incremented
VERSION by one further patchlevel

This adds belize3.sh, a system file for the newly-built belize3, using
the g++ compiler.

As a usage note, blitz requires python to build successfully.  As of
this writing, python is only available on belize3 with `module load
anaconda`.

This commit updates make_deps.sh to build newer versions of Blitz (1.0)
and fftw (3.3.9).  The 2010 version of Blitz no longer builds with the
newest versions of GCC, and there is no harm in updating FFTW.

The newest versions of Blitz (github head) require cmake to
build, and some systems still in use have old, incompatible versions of
cmake.  Blitz 1.0.2 requires python to complete its build process (some
files are auto-generated).

The new version of Blitz dropped the blitz::Vector type, being
equivalent to a 1-dimensional array, so it was replaced with
blitz::Array<type,1> instead.

Additionally, the Parformer (parallel transpose) code was adjusted to no
longer use MPI_UB to define the upper bound of the array section
datatype.  MPI_UB was deprecated in the MPI-2 standard and removed in
the MPI-3 standard, so SPINS could fail to build with some new MPI
libraries (OpenMPI 4.0.3 is confirmed to break).

Because this commit updates dependencies, the patch version is
incremented.

EOS Scripts

Added 3 EOS scripts: quadeos.cpp, lineos.cpp, and nleos.cpp, as well as a script to make the eos type a selectable option in the spins.conf. That is called eos.cpp.

See merge request !10

added g to spins.conf in /cases/derivatives/

See merge request !9

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