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

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.

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.

Also reorganize how some diagnostics are added to the file.
This is now a little clearer to read since similar diagnostics
are placed near each other.

In the previous merge, compilation of Sorter.o went missing from the
Makefile, and a typo was introduced in the gravity_current case file;
each would prevent a build from finishing.  These are fixed.

In certain cases, diagnostic computation required Nx/y/z > 1, but this
check was not repeated for adding the diagnostic output to the
respective file; this could result in unexpectedly writing 0 or
meaningless data to the file.

This change allows the gravity_current case to compute the v^2 component
of the kinetic energy term even if NY=1 when rot_f != 0; in that case
the solution can still develop a 2D geostrophic balance where v-velocity
balances a pressure gradient.

Additionally, the respective component sums are explicitly initialized to
0.

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

Some diagnostics are only computed in a specific configuration
(ie. a 2D field does not need to compute all three vorticity
components).

Creating a rank 3 matrix requires all three indices in the declaration
statement. This is only necessary when debugging, but should be explicit
wherever possible. Otherwise, too much time will be spent trying to
remember this fact when it matters.

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.

Diagnostic values (like total KE/ total enstrophy/ mass/ etc)
are often desired outputs at each time-step. These values
are easily printed to a txt file using two functions:
add_diagnostic and write_diagnostics.

add_diagnostic adds the name and value of a diagnostic into a
pair of strings which will be written into diagnostics.txt
which the function write_diagnostics.

Usage of add_diagnostic is as follows:
add_diagnostic(name, value, header, line);
This will add the string, 'name', onto the string, 'header', which
will be the header of the diagnostics.txt file. The double (or
int), 'value', will be added onto the string, 'line', which will
be a row (or line) in the diagnostics.txt file.

write_diagnostics will write these lines (header and line) into
diagnostics.txt.

The empty shell of check_timestep in BaseCase has been filled
with what was essentially the same thing in each case file.
Again, this is just more case file house cleaning.

A few ancillary functions have also been written to help.
The most important might be get_dt_max() which returns dt_max.
dt_max can either be specified in spins.conf or defined in the
case file based on the buoyancy frequency. Currently, if
dt_max > 0 and in spins.conf, then that value is used. Otherwise,
0.5/sqrt(N2_max) is used.

The re-definition of check_timestep in each case file can now be
removed so long as the associated ancillary functions and
parameters are included.

The generic code block to check the restart sequence is not needed
in the case file and has been moved into Options.cpp. This
streamlines the case file and makes a single copy for all other
case files to use.

The re-definition of get_restart_sequence() was missing in
gravity_current.cpp. This resulted in all restarts to read output
zero (*.0). Restarting will now properly read the output number
specified by restart_sequence.

gravity_current.cpp accepts filter parameters (f_cutoff, f_order,
f_strength) as optional input arguments. Easy adjustment of the
filter is useful when the flow become suddenly becomes too chaotic.

Parsing of expansion types in gravity_current.cpp moved to
Options.cpp. This is a general procedure that other case files
will and should make use of. It also simplifies the case file
to the specific set-up of that case.

Moved the section of gravity_current.cpp regarding the adjustment
of temporal values (restarting, initial_time, etc.) when restarting
from dump into Options.cpp as it is a standard piece of code and
should be in a centralized location.

The gravity_current case was located in a subdirectory, but
its #include directives had only one ".." in the path.  This
updates those directive to properly refer to the grandparent
subdirectory (src/), allowing the case to be built as:

make -j# cases/gravity_current/gravity_current.x

This case file is restartable and will dump all variables at the end of the requested computation time (stated in spins.conf) when run on SCINET or SHARCNET. The spins.conf enables the quick set-up of a parameter sweep as parameters are set within it and not within the case file which would need to be re-compiled.
This file will be used as a basis for the upcoming additions and changes to BaseCase.cpp and Science.cpp.