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Ds/nhsw

See merge request !1

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.

This commit amends Cheb_2dmg::resid_dot (dot-product of
residual vectors in the context of the 2D GMRES/multigrid
iteration) to perform the dot-product in the simplest way,
as a sum over grid elements.

Before this, the code (which is left in the file but
disabled by #if 1 / #else) tried to be clever and
evenly-weight contributions from the interior, the boundary
conditions, and the mean-pressure error (if the problem was
indeterminate).  This evidently caused the long-standing
problem of the GMRES inner iteration being far more
optimistic about error (as reported by LAPACK) than would be
computed by directly measuring the residual error.

This problem was ultimately discovered when the
doc_map_iwave case broke.  Even though this broken residual
code has been in SPINS since before it was
version-controlled via GIT, the map_iwave case would still
converge (and relatively quickly) when the multigrid
iteration had a relatively large coarse-solve size.

Git bisect pinned the broken documentation case on the
change that reduced the coase-grid size, which reduced the
GMRES convergence rates enough that the errors caused by
*this* problem broke convergence.

Since this change replaces the error norm calculations used
by GMRES, it should be treated with caution and mapped-grid
cases should have a mark-1-eyeball inspection of results for
a while.

--

Additionally, for debugging utility this change also
includes crude residual/basis output for the 2D GMRES
solver.  All current uses are commented out.

The addition of an analysis call on the initial data resulted
in the Nth time step to correspond with iteration N+1. This isn't
a problem, just dissatisfying.

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.

If dt_max is not given in the spins.conf, it is now explicitly
set to 0 so as to be adjusted later to use the buoyancy frequency.
The dt_max is also printed in the initialization for clarity.