Hypnotoad

---------------------

Bug fixes

- Check if an equilibrium can be gridded as a connected double-null before gridding. Prevents creation of invalid grids where second X-point is outside the first flux-surface in the SOL (104)\
By [John Omotani](https://github.com/johnomotani)

---------------------

Breaking changes

- Method for calculating zShift made more accurate. This will change the calculated zShift for the same input file (101)
- Default value for 'curvature_type' changed from "curl(b/B) with x-y derivatives" to "curl(b/B)". New default should be more accurate and more consistent when changing grid sizes, but will produce slightly different output from the same input file. If the old behaviour is needed, set 'curvature_type = "curl(b/B) with x-y derivatives"' explicitly (100)

New features

- Accuracy of calculation of zShift improved by integrating on FineContours rather than PsiContours (101)\
By [John Omotani](https://github.com/johnomotani)
- Circular, concentric flux surfaces magnetic geometry (100)\
By [John Omotani](https://github.com/johnomotani)
- Non-grid based method for calculating curvature (100)\
By [John Omotani](https://github.com/johnomotani)
- Parallelise most expensive loops (99)\
By [John Omotani](https://github.com/johnomotani)
- Fix position of start and end points of contours when refining and add more tolerance settings, to enable more reproducible grid generation (95)\
By [John Omotani](https://github.com/johnomotani)
- Options are saved as a YAML string in "hypnotoad_inputs_yaml" to make them easier to read in code later. (98)\
By [John Omotani](https://github.com/johnomotani)
- When exceptions are caught by the GUI, print the traceback as well as the exception message (95)\
By [John Omotani](https://github.com/johnomotani)

Testing

- Integrated tests, based on an analytic, connected double-null equilibrium (97, fixes 50)\
By [John Omotani](https://github.com/johnomotani)

Bug fixes

- Save all options to grid files. Previously only Equilibrium options were saved. Now also Mesh and nonorthogonal options (98)\
By [John Omotani](https://github.com/johnomotani)
- Setting to adjust extension of FineContours past targets, may help to avoid crashes on problematic equilibria (96)\
By [John Omotani](https://github.com/johnomotani)
- Diagnostic plots produced when some errors occur had invalid linestyles - use markers instead (95, fixes 94)\
By [John Omotani](https://github.com/johnomotani)

New features

- More robust calculation of distances in FineCountour.getDistance(), using
closest approach to line segments. Can be important for grids with sharp angles (87)\
By [Ben Dudson](https://github.com/bendudson)

Bug fixes

- Ensure FineContours always extend to the end of their parent PsiContour (86, fixes
84)\
By [Ben Dudson](https://github.com/bendudson)

Breaking changes

- Changed function used for determining radial positioning of grid points. Function now
guaranteed to be monotonic, so is more robust. However this does change the output
slightly compared to previous versions (64)\
By [John Omotani](https://github.com/johnomotani)
- Rename target_poloidal_spacing_length, nonorthogonal_target_poloidal_spacing_length,
nonorthogonal_target_poloidal_spacing_range,
nonorthogonal_target_poloidal_spacing_range_inner,
nonorthogonal_target_poloidal_spacing_range_outer renamed to *_target_all_*, because
extra settings were added to modify each of these parameters individually for each
target (75)\
By [John Omotani](https://github.com/johnomotani)

New features

- Python script to compare two grid files. Script uses xBOUT. Added to utils/
subdirectory of repo, and not installed with hypnotoad package (to avoid adding
dependency on xBOUT) (83)\
By [John Omotani](https://github.com/johnomotani)
- Option to start grid at upper-outer divertor instead of lower-inner (80)\
By [John Omotani](https://github.com/johnomotani)
- Smoothing copied from IDL hypnotoad for components of curvature vector (79)\
By [John Omotani](https://github.com/johnomotani)
- Check for unrecognised options in input files and raise an error if any are found
(76)\
By [John Omotani](https://github.com/johnomotani)
- Extra settings added so spacings can be controlled separately at each target (74)\
By [John Omotani](https://github.com/johnomotani)
- EquilibriumRegion.getSqrtPoloidalDistanceFunc() upgraded to ensure that when
it extrapolates the distance function is always monotonic. This is used when
y_boundary_guards is greater than 0 (73)\
By [John Omotani](https://github.com/johnomotani)
- Command line argument for hypnotoad_geqdsk to call pdb.set_trace() to make it
easier to debug exceptions with pdb (72)\
By [John Omotani](https://github.com/johnomotani)
- When grid file is created from a geqdsk input, save the filename, and the
contents of the geqdsk file to the grid file (71, closes 70)\
By [John Omotani](https://github.com/johnomotani)
- UUID unique identifier saved into each grid file (67, closes 66)\
By [John Omotani](https://github.com/johnomotani)

Bug fixes

- String outputs written as file attributes rather than variables (69, fixes 68)\
By [John Omotani](https://github.com/johnomotani)
- Failure when target_poloidal_spacing_length set to number (rather than the
default None) when y_boundary_guards is non-zero (64)\
By [John Omotani](https://github.com/johnomotani)
- BoutMesh options now settable in GUI (63)
By [John Omotani](https://github.com/johnomotani)
- Changing settings in File->Preferences caused GUI to crash (62, fixes 61)\
By [John Omotani](https://github.com/johnomotani)

New features

- ``y-coord`` and ``theta`` poloidal coordinates written out by ``BoutMesh`` (51, fixes 49)\
By [John Omotani](https://github.com/johnomotani)

Bug fixes

- Timeout if FineContour.refine() takes too long. Length of timeout set by refine_timeout option (58)\
By [John Omotani](https://github.com/johnomotani)

Fixes support for non-orthogonal grids, adds regridding non-orthogonal functionality to GUI.

https://github.com/boutproject/hypnotoad/blob/master/doc/whats-new.md#020-25th-june-2020