Tests and examples for Bessel beams

[stefaniagl]

Description

Added tests and examples of the usage of Bessel beams.

Related issues

Related to #209

Types of changes

• Bugfix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)

Checklist

• I have read the contributing guidelines
• The new code complies with the existing code style.
• The code compiles correctly in all relevant regimes (at least, make seq)
• The new code does not rely on any Fortran or C++ sources or is disabled by NO_FORTRAN or NO_CPP preprocessor macros, respectively.
• The change neither adds or removes files; otherwise, these changes are reflected in README.md in corresponding folders.
• No warnings appear during debug compilation (at least, make seq OPTIONS=DEBUG, but better devtools/build_debug) or they are discussed below
• Tests pass locally with my changes (at least, sh comp2exec seq in tests/2exec, but better devtools/test_new [seq]). If any errors appear, they are discussed below.
• I have added tests that prove my fix is effective or that my feature works. And these tests pass. This includes new command line in suite files in tests/2exec (and potentially new ignore patterns). In some cases, it is desirable to add new tests to tests/equiv.
• I have added/extended necessary documentation (if appropriate). If suggesting changes to the manual, I have used "Track changes" in the doc file.
• I have looked through all changes introduced by this pull request (line by line), using git diff or, better, some GUI tool, to ensure that no unexpected changes are introduced.

Further comments

[myurkin]

I have just pushed some minor changes. Additionally the following need to be done:

• synchonize with current master

test/equiv/bessel

• move them to one folder above. Hence, merge corresponding README files.
• add more digits to the used pi constant (maybe use some built-in variable)
• try to make the output agree with smaller threshold, e.g., 1e-8
• hide ADDA output when running tests (direct it to /dev/null but make portable)
• further reduce output to stdout from the script itself, so only the essential information is given (like compared lines and whether the test passed)
• more detailed output would go only to results.txt (as now), but this file should be added to .gitignore (in the same folder)

examples/bessel/

• add some basic comments before "run_options = ...", so an user can play with it without referring to the manual
• all output files should be added to .gitignore (create the latter in this folder)
• the plot of incident field should be accurate in what is shown (now it is the squared amplitude)
• maybe add the specific command line for options 1 and 2 on top of the plot, so the latter would be self-contained
• add more description in README.md, including the common parameters of a simulation (like "wavelength-sized sphere"), which files are produced, and what is included in the graph. Use Markdown for formatting where appropriate.

examples/papers/

• update README.md with a short description similar to the already present for the WKBr (in the current master)
• rename folder bessel into 2022_bessel
• 2022_bessel/README.md should describe all files present in this folder (also see the WKBr example)
• it would be great to have a separate Python script for each of Figs. 12-15 from the paper (named by this figures). They can use some common script to not duplicate the code.

[myurkin]

I have pushed some more corrections. Remaining issues are:

• for equiv tests, all the computed differences should be relative. Then levels of 1e-8 or even 1e-9 can be achieved. The text in comments, README, and output should also be changed to indicate that the differences are relative.
• ensure that there are end-of-lines at the end of all files (otherwise GitHub shows warnings when looking at changes)

examples/papers/2022_bessel:

• scripts does not work if dda/ folder does not exist (should be created by the script itself). Same problem with extrapolation/ in fig14.
• fig12 produces warning, and minor ticks are missing on vertical axes of the left subfigure.

  d:\Tmp\bessel\examples\papers\2022_bessel\fig12_sphere.py:39: UserWarning: This figure includes Axes that are not compatible with tight_layout, so results might be incorrect.
    plt.tight_layout()

• the same warning appears in all figures.
• the comment in the beginning of fig15_cube.py is incorrect.