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Merge SP contributions #14

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Merge SP contributions #14

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@Phoelionix
Syncing misc changes to the git
084f484
@Phoelionix
added some inputs
c7a7fe0
@Phoelionix
sorting out convergence in Ar HF code
cbd6a08
@Phoelionix
Updated TODO in readme
0228dbe
@Phoelionix
Added reflection file conversion to scalemap (.sca) format for CCP4 c…
30ce05d 
…ompatibility
@Phoelionix
Added failsafe for output size in scattering sim
183c8bb
@Phoelionix
Fixed sector plot angle range issue
2f71735
@Phoelionix
Fixed colours of interactive in the wake of some panicked temporary c…
e731322 
…hanges
@Phoelionix
Updated interactive plotting to be much clearer
da5bf7f
@Phoelionix
Fixed elevated intensity trace
4cbfbda
@Phoelionix
Fixed issue with interactive not plotting to final time.
a77f463
@Phoelionix
total ionisation plotting for comparing effect of photon energy
ac72a4e
@Phoelionix
Fixed up look of R scattering pixel sampling plots
ba3f7a4
@Phoelionix
Total ionisation for multiple batches on same axes
acd7a3f
@Phoelionix
Added Zr Auger support grid
ab39d60
@Phoelionix
Streamlined process: total ionisation plot now automatically chooses …
c04ceaa 
…the latest run number.
@Phoelionix
damage_comparison.py -> damage_landscape.py
17d2c9d
@Phoelionix
total_ionisation_plot->goldilocks_plotting
068561e
@Phoelionix
Integrated R factor plotting with goldilocks plotting
6f27b53
@Phoelionix
goldilocks plot - Making the subplot canvas a fixed size
dd2b634
@Phoelionix
minor fix
198b4af
@Phoelionix
Changed sim so that knot checkpoints behave a bit more intuitively, i…
87adbe3 
…nterpolating forwards from the checkpoint rather than backwards. Also means output now includes interpolated states from checkpoint loading (rather than using the original uninterpolated staets). Also prevented shrinkage in dynamic grid when new peak is in the dangerous low energy region.
@Phoelionix
Seprated meaning of initial state and zero state in the code. Cleaned…
783e2e0 
… up a bit. Should be less confusing now.
@Phoelionix
Plotting for net ionisation rate
6323a67
@Phoelionix
Squashed bug from yesterday's commit
e780bc7
@Phoelionix
Can now plot snapshot based on plotly interactive code and it looks n…
39026f9 
…ice.
@Phoelionix
removed unwanted axis title from inset plot
0161120
@Phoelionix
Prevent inset from being used where not supported
0dfa49c
@Phoelionix
Fixed terminal from being messed up by saves (I think)
7e54f64
@Phoelionix
Should be displaying properly now
c45aea9
@Phoelionix
Undid bugged parallelisation changes to bound secondary ion.
ca0a861 
These changes weren't making a big performance improvement anyway.
@Phoelionix Phoelionix force-pushed the working_branch branch 2 times, most recently from 78c777c to f9f0b1f Compare January 18, 2025 01:13
@Phoelionix Phoelionix force-pushed the working_branch branch 2 times, most recently from 371a2fc to ffe9fd7 Compare January 21, 2025 00:58
@Phoelionix
Fixed handling of plotting split continuums
c4ee4c4 
also improved orb densities plotting
@Phoelionix Phoelionix force-pushed the working_branch branch 3 times, most recently from 57667d4 to fd806ca Compare January 21, 2025 01:02
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@Phoelionix