Fix a number of bugs/corner cases - #261

Merged

astrofrog merged 32 commits into

hyperion-rt:mainfrom

astrofrog:bug-fixes

Jul 25, 2026

Commits on Jul 25, 2026

Compare recomputed AMR cell indices in in_correct_cell instead of the stale unique cell ID which made the off-wall check always pass
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Clamp random cell and dust indices to a minimum of 1 so a random number of exactly zero cannot produce an out-of-bounds index of 0
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Accumulate the PDA exact solver off-diagonal coefficient so both phi walls contribute when they wrap to the same neighbour
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Add missing public declaration for write_grid_5d to the 1D grid IO template and regenerate grid_io_1d.f90
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Remove stray space in the AMR read_grid_3d dataset path so luminosity maps can be read
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Fix octree find_cell bounds checks that compared y instead of x and z against xmax and zmax
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Fix sign of lower-wall distances in octree distance_to_closest_wall so it no longer always returns zero
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Reset the sublimate_dust cell counter per dust type so printed counts are not accumulated across dust types
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Zero out specific_energy_spectrum in zero-volume cells to avoid NaN from division by zero cell volume
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Use 8-byte integers for killed photon counters to avoid overflow on large runs
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Initialize the converged flag before the Lucy iteration loop so runs without convergence checking do not write an undefined value
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Send worker timings with a blocking send from a saved variable instead of a non-blocking send of an expression temporary
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Fix character table column broadcast to send the full string buffer instead of only the first n1 characters
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Raise an error in AlphaDisk.density when the discretized disk mass is zero instead of silently producing NaNs
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Fix AmbientMedium validation to check rho instead of the density method
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Fix factor of 2 overestimate in Ulrich envelope midplane cumulative density inside the centrifugal radius
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Reverse decreasing wavelength arrays before loglog interpolation so MieXDust NaN repair works instead of raising a bounds error
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Raise NotImplementedError instead of calling the NotImplemented singleton in Source.get_spectrum
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Fix off-by-one slice bound that dropped the second-to-last point when integrating up to the last tabulated x in the four subset integrators
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Fix AMR external quantity links to use the grid index instead of the level index in the per-grid path
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Fix VoronoiGrid.__setitem__ to check point geometry instead of the nonexistent refined attribute and copy bounds when cloning geometry
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Fix voronoi_grid.plot to work on Python 3 by listifying range and using integer division for np.split
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Fix Orion importer endianness check that compared a list to a range and always failed on Python 3
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Fix _read_monochromatic to read the monochromatic_energy_threshold attribute written by _write_monochromatic
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Fix use_image_config to restore binned image configuration from the group_00001 subgroup where it is written
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Normalize negative group indices in get_sed and get_image before building the HDF5 group name
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Make get_available_components use the same zero-based iteration numbering as get_quantities
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Fix set_convergence to use its convergence argument instead of always enabling convergence checking
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Fix misspelled central_spectral_coords attribute assignment in Filter.from_hdf5_group so nu0 survives the HDF5 round trip
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Store and propagate the min argument in OptThinRadius instead of discarding it
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Add regression tests for the fixes on this branch
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Build AMR external link paths with posixpath so HDF5 object paths do not get backslash separators on Windows
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