14. Release history¶

14.1. Bug fixes¶

14.2. New features¶

Radial grid line construction can recover from failure and generate a rough grid to help visual inspection when option follow_perpendicular_recover is set to True (#175)
A View menu enables the grid plot to be customised, with cell edges, corners, grid lines and other components (#176).
penalty_mask is calculated and written to the grid file, based on intersection of the grid with the wall. This enables immersed boundary conditions.
Wall coordinates are written to output grid as closed_wall_R and closed_wall_Z (#176)

14.3. 0.5.2 (13th March 2023)¶

Bug fixes¶

Document that editable installs are recommended for developers in manual and exception message (#167)
By John Omotani

New features¶

Save R,Z locations for all four corners of each cell (#168)
By John Omotani
PsiContour.plot() and FineContour.plot() can be called with an ax argument, and passing psi is optional (#163)
By Ben Dudson

14.4. 0.5.1 (18th January 2023)¶

New features¶

Command line utility to get flux surfaces from a geqdsk file and save them to NetCDF (#156)
By John Omotani

14.5. 0.5.0 (12th January 2023)¶

Breaking changes¶

Renamed command line programs to make the style consistent. All now use ‘-’ as a separator, not ‘_’ (#142)
By John Omotani
Change how initial spacing of points on separatrix for nonorthogonal grids is calculated (this spacing is used to construct the underlying orthogonal grid). Now use weights that are just {cos(0.5*pi*i/index_length)**2,sin(0.5*pi*i/index_length)**2} rather than trying to construct a function that will give the same spacings when called with the ‘orthogonal spacing’ that came from the initial call passed in as sfunc_orthogonal. This means that the underlying orthogonal grid does not rely at all on nonorthogonal_* settings, so removes an issue where some grids could only be constructed by generating first with one set of nonorthogonal_* settings, then changing them and regridding. It also removes the possibility of a “Weight too small. Suggest increasing poloidal ‘range’ settings” error, since the branch that produced that error no longer exists. Does change the nonorthogonal grids that will be produced by hypnotoad, although the integrated tests pass without updating the expected results, so the changes should be small (less than 1e-9 for the integrated test cases) (#138)
By John Omotani

Bug fixes¶

Catch error when psi_sol_inner is set wrong. Add suggestions to ‘gradient at end should be positive’ error message (#130)
By Ben Dudson
Fix psi_axis check when reverse_current=True (#131)
By John Omotani
Errors when setting options could crash GUI. Can now change string options in GUI. Reset to old value if invalid value is passed for some option. Type name is actually shown in error message pop-up when incorrect type is passed (#134)
By John Omotani
Fix potential error in check of X-point psi vs. psinorm_sol (#143)
By John Omotani

New features¶

Create a manual for hypnotoad (#145)
By John Omotani
Convenience script for making a plot of an equilibrium from a geqdsk file (#139)
By John Omotani
If an int (or other Number) literal is passed to a float-type option, it is converted implicitly instead of causing an error. (#134)
By John Omotani

14.6. 0.4.4 (26th October 2022)¶

Bug fixes¶

Fix for circular geometries with non-constant q (#120)
By John Omotani

New features¶

Command to recreate input file and gfile from a grid file (#119)
By John Omotani
Save all variables at xlow positions (as *_xlow), as these can be used by BOUT++ to create CELL_XLOW Coordinates objects. Also save the positions of the cell corners (Rxy_corners and Zxy_corners) as these may be useful for plotting (#118)
By John Omotani
Add executable hypnotoad_plot_grid_cells that takes a grid file as input and uses xbout to plot the grid cells from the newly added corner positions (#118)
By John Omotani

14.7. 0.4.3 (25th December 2021)¶

Bug fixes¶

Small fixes and minor optimizations for nonorthogonal gridding (#113)
By John Omotani
Pass psi to keyword argument where this update had been missed previously (#113)
By John Omotani
Fix plotting of poloidal lines in Mesh.plotPoints() (#113)
By John Omotani
Minor fixes updating TORPEX case (#106)
By John Omotani
Fix crash in hypnotoad-gui if input file did not contain an ‘orthogonal’ setting (#106)
By John Omotani

New features¶

Save poloidal distances along psi contours to grid file (#116)
By John Omotani
Option to reverse sign of toroidal magnetic field Bt for TokamakEquilibrium (#114)
By John Omotani
Enable DCT interpolation scheme in TokamakEquilibrum, can be selected with new option psi_interpolation_method (#113)
By John Omotani
Add xpoint_offset option for TORPEX case (#113)
By John Omotani
Clean up of examples. Input files from examples/tokamak can now be used with hypnotoad-gui (#106)
By John Omotani
psi_axis and psi_bdry are added to the grid file for post-processing. The calculated values should be consistent with the EFIT data (#112)
By Qian Xia

14.8. 0.4.1 (26th May 2021)¶

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
Correct setting of ixseps1 and ixseps2 for upper disconnected double null case - should have ixseps1>ixseps2 but previously had ixseps1<ixseps2 (#109)
By John Omotani

14.9. 0.4.0 (26th May 2021)¶

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
Circular, concentric flux surfaces magnetic geometry (#100)
By John Omotani
Non-grid based method for calculating curvature (#100)
By John Omotani
Parallelise most expensive loops (#99)
By John Omotani
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
Options are saved as a YAML string in “hypnotoad_inputs_yaml” to make them easier to read in code later. (#98)
By John Omotani
When exceptions are caught by the GUI, print the traceback as well as the exception message (#95)
By John Omotani

Testing¶

Integrated tests, based on an analytic, connected double-null equilibrium (#97, fixes #50)
By John Omotani

Bug fixes¶

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

14.10. 0.3.1 (11th February 2021)¶

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

Bug fixes¶

Ensure FineContours always extend to the end of their parent PsiContour (#86, fixes #84)
By Ben Dudson

14.11. 0.3.0 (25th January 2021)¶

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
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

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
Option to start grid at upper-outer divertor instead of lower-inner (#80)
By John Omotani
Smoothing copied from IDL hypnotoad for components of curvature vector (#79)
By John Omotani
Check for unrecognised options in input files and raise an error if any are found (#76)
By John Omotani
Extra settings added so spacings can be controlled separately at each target (#74)
By John Omotani
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
Command line argument for hypnotoad_geqdsk to call pdb.set_trace() to make it easier to debug exceptions with pdb (#72)
By John Omotani
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
UUID unique identifier saved into each grid file (#67, closes #66)
By John Omotani

Bug fixes¶

String outputs written as file attributes rather than variables (#69, fixes #68)
By John Omotani
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
BoutMesh options now settable in GUI (#63) By John Omotani
Changing settings in File->Preferences caused GUI to crash (#62, fixes #61)
By John Omotani

14.12. 0.2.1 (12th January 2021)¶

New features¶

y-coord and theta poloidal coordinates written out by BoutMesh (#51, fixes #49)
By John Omotani

Bug fixes¶

Timeout if FineContour.refine() takes too long. Length of timeout set by refine_timeout option (#58)
By John Omotani

14.13. 0.2.0 (25th June 2020)¶

New features¶

Button allowing grid to be regenerated in the gui after nonorthogonal spacing options are changed (#26)
By John Omotani

Bug fixes¶

More robust generation of non-orthogonal grids for tokamak cases (#26)
By John Omotani

14.14. 0.1.4 (21st June 2020)¶

Internal changes¶

Make compatible with v5.13 of pyside2 (#45)
By John Omotani

14.15. 0.1.3 (20th June 2020)¶

Internal changes¶

Warn instead of failing in case of ImportError when setting “Qt5Agg” backend (#44)
By John Omotani

14.16. 0.1.2 (20th June 2020)¶

Internal changes¶

Use argparse in command line scripts (#42)
By John Omotani

14.17. 0.1.1 (9th June 2020)¶

New features¶

For orthogonal grids, save hy as ‘hthe’. Allows backward compatibility with codes that compute metric coefficients for themselves. hy and hthe definitions are the same for orthogonal grids. They differ for non-orthogonal grids, so hy is not written as ‘hthe’ for non-orthogonal grids, to prevent silent errors (#39)
By John Omotani
Options have associated doc attributes, visible as tool-tips in the GUI (#33)
By John Omotani
Add preferences dialog to GUI (#25)
By Peter Hill and John Omotani
Catch errors in HypnotoadGui.run(), allows changing settings and pressing Run button again if there was an error in grid generation (#24)
By John Omotani and Peter Hill
Plot wall in gui window (#23)
By John Omotani

Bug fixes¶

If an empty string is passed to a value in the options table of the GUI, resets the option to its default value. Previously this caused a crash (#25)
By John Omotani

Internal changes¶

options package dependency removed, replaced by hypnotoad.utils.OptionsFactory, which creates immutable Options objects. WithMeta class used to store the value of each option along with (optionally) a doc attribute, required type, list of allowed values, and list of checks that the value must pass (else raise an exception) (#33)
By John Omotani
Make options table keys in HypnotoadGui immutable. Also makes the use of Options object in Equilibrium/TokamakEquilibrium more consistent by ensuring self.user_options has only been delegated once from TokamakEquilibrium.default_options (i.e. the push() method has only been used once, otherwise update() or set() are called) (#25)
By John Omotani

14.18. 0.1.0 (24th April 2020)¶

New features¶

Github Action to upload hypnotoad to PyPi on release (#19)
By John Omotani
Version number auto-detected from git tags using versioneer (#18)
By John Omotani
Graphical user interface, using Qt.py (#17)
By Peter Hill
Github Actions automatically run pytest, flake8 and black (#10)
By John Omotani
Support for tokamak grids (#2)
By Ben Dudson

Bug fixes¶

Set wall=[] instead of wall=None when there is no wall (#12 #9) By John Omotani

Documentation¶

doc/whats-new.md documents changes (#22)
By John Omotani
doc/developer/RELEASE_HOWTO.md specifies release process By John Omotani

Internal changes¶

Rename package and repo from ‘hypnotoad2’ to ‘hypnotoad’ (#21)
By John Omotani

14.19. 0.0.0 (24th March 2020)¶

Python grid generator for BOUT++, supporting orthogonal or non-orthogonal grids. Working for TORPEX X-point configuration. By John Omotani