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Merge SP contributions #13

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Merge SP contributions #13

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Phoelionix and others added 30 commits August 27, 2023 14:49
@Phoelionix
Update README.md
d775235
@Phoelionix
Update README.md
344e885
@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 and others added 30 commits March 10, 2024 09:36
@Phoelionix
Correct units for input omega being saved
e2cbe40
@Phoelionix
Identified a bug with HF that occurs in Greens Method when HF code mo…
d05311a 
…dels heavier elements under HF potential. i = 11164 config with Zn, note how W = 0.
@Phoelionix
Saving params that are to be run across targets of differing composit…
f017c53 
…ions
@Phoelionix
Flagging issue with Zn HF code
314ae42
@Phoelionix
Oops updating makefile with boost libraries.
a7ac7f5 
Necessary for accessing the saved photoion. data. If it's a problem, an implementation using a single file, rather than one for each X-ray frequency,  would make this unnecessary.
@Phoelionix
input update
51b2c78
@Phoelionix
Sync misc changes for merge
1ee2194
@Phoelionix
Merge pull request #6 from Phoelionix/working_branch
a90552e 
Merged working branch
ignore .out
8c3672c
@Phoelionix
Resolved missed stashed changes
055851b
@Phoelionix
Small misc changes to damage landscape plotting data handling
52f6c0a
@Phoelionix
Fixed foolish mistake of unlocking all electron shells for calculation.
04fbe0b
@Phoelionix
critical todo for fixing issue introduced by last commit
f1167b1
@Phoelionix
Fixed issue where program would attempt to load forbidden configurati…
9d8159b 
…ons.

Slightly suspicious that the fix was so easy but it seems to be working now.
@Phoelionix
Misc changes for merging with HPC
ef3beae
@Phoelionix
Suspicions were correct. Now generates separate decay rate files for …
e56282b 
…each set of allowed configs. Also flagged that the implementation of multiple energies wasn't properly accounting for this.
@Phoelionix
Removed assertion that was misunderstanding the code's logic
dfc26f5
@Phoelionix
syncing scripts and new inputs
5a78262
@Phoelionix
misc sync changes
35fa100
@Phoelionix
Buggy implementation of split eii
29b72ce
@Phoelionix
update period now independent of early cutoff time.
301a96b
@Phoelionix
Continuing to work on bugs for split continuum, plotter_core.py updat…
d1e2bc9 
…ed scrappily to allow for combining cascade continuums (e.g. CNO)
@Phoelionix
sync
a68d2c8
@Phoelionix
sync2
b550073
@Phoelionix
Got split continuum working. Now tracks cascades spawned by each elem…
f44a530 
…ent.
@Phoelionix
Fixed graphing 2 subplots + y axis starts at 0 by default for element…
6cf2dea 
… charge plot
@Phoelionix
Added (very rough) I3C inputs
706dd14
@Phoelionix
Merge pull request #8 from Phoelionix/split_eii
3cbd97d 
Split eii
@Phoelionix
Update README.md
4de3812
@Phoelionix
Updated config file to make program more generally compatible
662bd14
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2 participants
@Spuriosity1 @Phoelionix