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Merge SP contributions#13

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Spuriosity1 wants to merge 133 commits intoSpuriosity1:masterSpuriosity1/AC4DC:masterfrom Phoelionix:masterPhoelionix/AC4DC:masterCopy head branch name to clipboard

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Commits

Commits on Aug 27, 2023

• Update README.md

  Phoelionix

  authored
  d775235

• Update README.md

  Phoelionix

  authored
  344e885

Commits on Nov 13, 2023

• Syncing misc changes to the git

  Phoelionix

  committed
  084f484

Commits on Nov 14, 2023

• added some inputs

  Phoelionix

  committed
  c7a7fe0

• sorting out convergence in Ar HF code

  Phoelionix

  committed
  cbd6a08

Commits on Nov 18, 2023

• Updated TODO in readme

  Phoelionix

  committed
  0228dbe

• Added reflection file conversion to scalemap (.sca) format for CCP4 compatibility

  Phoelionix

  committed
  30ce05d

• Added failsafe for output size in scattering sim

  Phoelionix

  committed
  183c8bb

Commits on Nov 19, 2023

• Fixed sector plot angle range issue

  Phoelionix

  committed
  2f71735

Commits on Nov 21, 2023

• Fixed colours of interactive in the wake of some panicked temporary changes

  Phoelionix

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  e731322

• Updated interactive plotting to be much clearer

  Phoelionix

  committed
  da5bf7f

Commits on Nov 22, 2023

• Fixed elevated intensity trace

  Phoelionix

  committed
  4cbfbda

• Fixed issue with interactive not plotting to final time.

  Phoelionix

  committed
  a77f463

Commits on Nov 23, 2023

• total ionisation plotting for comparing effect of photon energy

  Phoelionix

  committed
  ac72a4e

• Fixed up look of R scattering pixel sampling plots

  Phoelionix

  committed
  ba3f7a4

Commits on Nov 24, 2023

• Total ionisation for multiple batches on same axes

  Phoelionix

  committed
  acd7a3f

Commits on Nov 25, 2023

• Added Zr Auger support grid

  Phoelionix

  committed
  ab39d60

Commits on Nov 26, 2023

• Streamlined process: total ionisation plot now automatically chooses the latest run number.

  Phoelionix

  committed
  c04ceaa

• damage_comparison.py -> damage_landscape.py

  Phoelionix

  committed
  17d2c9d

• total_ionisation_plot->goldilocks_plotting

  Phoelionix

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  068561e

• Integrated R factor plotting with goldilocks plotting

  Phoelionix

  committed
  6f27b53

Commits on Nov 28, 2023

• goldilocks plot - Making the subplot canvas a fixed size

  Phoelionix

  committed
  dd2b634

• minor fix

  Phoelionix

  committed
  198b4af

Commits on Dec 1, 2023

• Changed sim so that knot checkpoints behave a bit more intuitively, interpolating forwards from the checkpoint rather than backwards. Also means output now includes interpolated states from checkpo…

  Show description for 87adbe3
  Phoelionix

  committed
  87adbe3

Commits on Dec 2, 2023

• Seprated meaning of initial state and zero state in the code. Cleaned up a bit. Should be less confusing now.

  Phoelionix

  committed
  783e2e0

• Plotting for net ionisation rate

  Phoelionix

  committed
  6323a67

• Squashed bug from yesterday's commit

  Phoelionix

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  e780bc7

• Can now plot snapshot based on plotly interactive code and it looks nice.

  Phoelionix

  committed
  39026f9

• removed unwanted axis title from inset plot

  Phoelionix

  committed
  0161120

Commits on Dec 3, 2023

• Prevent inset from being used where not supported

  Phoelionix

  committed
  0dfa49c

Commits on Dec 4, 2023

• Fixed terminal from being messed up by saves (I think)

  Phoelionix

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  7e54f64

• Should be displaying properly now

  Phoelionix

  committed
  c45aea9

Commits on Dec 5, 2023

• Fixed issue with loading checkpoints without updating n.

  Phoelionix

  committed
  4c6fb6f

• Split fit for goldilocks plot, + plotting orbitals

  Phoelionix

  committed
  4690589

• live plot updating period can now be set in mol file

  Phoelionix

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  add3b0e

• removed some vestigial print funcs

  Phoelionix

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  eb7225b

• Various bug fixing for simulation loading with checkpoint changes

  Phoelionix

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  3a1330c

Commits on Dec 6, 2023

• Trying to reproduce galli again

  Phoelionix

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  34696f8

• Should log grid changes properly again.

  Phoelionix

  committed
  5ee11ba

• Can now use regions with lower minimum MB knots

  Phoelionix

  committed
  4cc7f72

Commits on Dec 7, 2023

• Finished allowing min gp for MB distribution to be preset dependent.

  Phoelionix

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  5f154b1

• log mb region option

  Phoelionix

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  d136a7e

Commits on Dec 13, 2023

• Goldilocks relative difference

  Phoelionix

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  6793f0d

Commits on Dec 14, 2023

• Started tidying up, + plotting against the dopant's low photoelectron energy

  Phoelionix

  committed
  1eaba73

• Nice form for photo-e indep variable goldilocks

  Phoelionix

  committed
  e8fa718

• electron source can now be added in .mol input files

  Phoelionix

  committed
  19e7081

• input sync

  Phoelionix

  committed
  da38dac

• Correct units for electron source energy

  Phoelionix

  committed
  c831907

• Fixed sign issue for source + new log grid template!

  Phoelionix

  committed
  7fad561

• Log grid template adjusted + fixed issue with using int that was gaslighting me...

  Phoelionix

  committed
  8dfd142

• forgot to push /include.

  Phoelionix

  committed
  430034a

• fix for multi-element electron source

  Phoelionix

  committed
  e99c46b

Commits on Dec 15, 2023

• Generate electron source param batches, and overhauled batch generation logic to make future such extensions easier

  Phoelionix

  committed
  c3d7215

• only log MB grid

  Phoelionix

  committed
  c1df179

• preset updated properly now (meaning it probably wasn't actually using lower dirac regions properly before)

  Phoelionix

  committed
  8643964

• Fixed issue with artificial source region not being supported

  Phoelionix

  committed
  7f8608f

• Small batch generation fix

  Phoelionix

  committed
  4179a4c

Commits on Dec 16, 2023

• t for the electron source now needs to be LESS than the cutoff time. How did I manage this...

  Phoelionix

  committed
  ced26cf

• source duration now correctly read from mol input...

  Phoelionix

  committed
  01c01c2

Commits on Dec 17, 2023

• Misc QOL to goldilocks plotting

  Phoelionix

  committed
  5320013

Commits on Dec 18, 2023

• Photoionisation rates tracking

  Phoelionix

  committed
  9441b75

• Silenced error messages due to comparison of unsigned and signed ints

  Phoelionix

  committed
  00e7638

• Oops accidentally silenced critical code

  Phoelionix

  committed
  4320e40

• Further suppression of errors

  Phoelionix

  committed
  3a8d4a4

• Fixed minor output issue with photo rate

  Phoelionix

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  fce0362

• Photoion. rate plotting

  Phoelionix

  committed
  8342863

• Sync scripts

  Phoelionix

  committed
  ff09a4e

• Can now specify elements for which to ignore secondary ionisation. For targets with trace amounts of heavy elements, can greatly speed up the solver with little loss in accuracy.

  Phoelionix

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  b9e1d70

• Updated batch generation to copy exclusions in template file

  Phoelionix

  committed
  08f94ca

Commits on Dec 19, 2023

• Merge pull request #4 from Phoelionix/working_branch

  Show description for 53a41e8
  Phoelionix

  authored
  53a41e8

Commits on Dec 20, 2023

• Electron source can now be above photon energy.

  Phoelionix

  committed
  1591442

Commits on Dec 23, 2023

• Simulation can reset after first grid update to use the more reliable dynamically determined grid, rather than the guess. Also a lot of code tidying up.

  Phoelionix

  committed
  c97d7d9

• Reinitialised simulations now exit properly without weirdly restarting and failing.

  Phoelionix

  committed
  198dc4c

Commits on Dec 24, 2023

• Fixed dirac peak identification and constant source emission rate.

  Show description for 7fd07c2
  Phoelionix

  committed
  7fd07c2

• Merge pull request #5 from Phoelionix/working_branch

  Show description for 510b894
  Phoelionix

  authored
  510b894

• Turned off problematic assertion in dynamic grid code

  Phoelionix

  committed
  d955810

Commits on Dec 25, 2023

• static grid for high energy region because it's just too clunky for electron source. Also program no longer allows you to pass an invalid grid preset

  Phoelionix

  committed
  c9a2ed9

• Slight adjustments to new grid

  Phoelionix

  committed
  b3e95db

• trying more dense centre for elec source region

  Phoelionix

  committed
  0661462

Commits on Dec 26, 2023

• Streamlined working with batches in goldilocks plotting and sim param pulling. Still clunky however.

  Phoelionix

  committed
  bd263c6

Commits on Dec 27, 2023

• Goldilocks plotting now saves generated data

  Show description for 66b0709
  Phoelionix

  committed
  66b0709

• Goldilocks: Saving separate scattering targets' data + merge deeply

  Phoelionix

  committed
  984f561

Commits on Dec 28, 2023

• Patched over issue with square pulse when timespan factor not specified

  Phoelionix

  committed
  b56f65b

• Floating point assertion error fixed

  Phoelionix

  committed
  aaf319f

Commits on Dec 30, 2023

• unbroke interactive legend

  Phoelionix

  committed
  96f0623

Commits on Jan 10, 2024

• Can now quick and dirtily plot the damage from a full batch with selection of parameters. Also damage landscape for average carbon charge supported now

  Phoelionix

  committed
  111fa34

Commits on Jan 12, 2024

• Adding new measures of damage to plot is now far simpler/automatic (with regards to data analysis modules). NOTE still have to check if damage comparison plot needs to be patched

  Phoelionix

  committed
  0775b7d

• max q no longer allowed to be above any pixel's

  Phoelionix

  committed
  0845aad

• Various plotting bugs relating to scattering resolution limits fixed.

  Phoelionix

  committed
  070c872

Commits on Jan 14, 2024

• Fixed some silly issues in reload_grid()

  Phoelionix

  committed
  a56ef2e

• Slight fix for prior patch for reload_grid, reverting some changes. The only issue was transient_y was initialised with the first checkpoint step, rather than the last one (explaining jumps in ioni…

  Show description for 7d1dd65
  Phoelionix

  committed
  7d1dd65

• Reverted checkpoint patch commits

  Phoelionix

  committed
  355f4c5

• Finally properly fixed checkpoint loading.

  Phoelionix

  committed
  ac1b57c

Commits on Jan 15, 2024

• Log intensity ratio damage measure added for damage_landscape.py.

  Phoelionix

  committed
  85a8e0d

Commits on Jan 26, 2024

• orbital charge legend for dashed and solid

  Phoelionix

  committed
  bed772f

• Units and inset plot axis title for interactive

  Phoelionix

  committed
  8aa20d8

Commits on Jan 27, 2024

• Separating user input from interactive plotting handling, adding in interactive, snapshot, and animation .py scripts, with the generate_interactive.py core code renamed to interactive_handler.py

  Phoelionix

  committed
  370fad7

Commits on Mar 7, 2024

• General sync

  Phoelionix

  committed
  65d2467

Commits on Mar 8, 2024

• batch store photoion. data

  Phoelionix

  committed
  4d16763

• Massive performance improvement - HF code now only ever needs to be run once over a batch of simulations. Not quite finished, still need to implement interpolation. However the core logic is implem…

  Show description for b418ca3
  Phoelionix

  committed
  b418ca3

• A few fixes for the rate loading implementation, which wasn't working.

  Phoelionix

  committed
  3b9cb0a

• Forcing recompute of EII if needed. Note that the photoion. calc isn't correct at present!!!

  Phoelionix

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  55f1604

• Producing correct photoion. rates again

  Phoelionix

  committed
  d4aedf6

Commits on Mar 9, 2024

• Correct units for input omega being saved

  Phoelionix

  committed
  e2cbe40

Commits on Mar 10, 2024

• Identified a bug with HF that occurs in Greens Method when HF code models heavier elements under HF potential. i = 11164 config with Zn, note how W = 0.

  Phoelionix

  committed
  d05311a

Commits on Mar 11, 2024

• Saving params that are to be run across targets of differing compositions

  Phoelionix

  committed
  f017c53

• Flagging issue with Zn HF code

  Phoelionix

  committed
  314ae42

• Oops updating makefile with boost libraries.

  Show description for a7ac7f5
  Phoelionix

  committed
  a7ac7f5

Commits on Mar 13, 2024

• input update

  Phoelionix

  committed
  51b2c78

• Sync misc changes for merge

  Phoelionix

  committed
  1ee2194

• Merge pull request #6 from Phoelionix/working_branch

  Show description for a90552e
  Phoelionix

  authored
  a90552e

• ignore .out

  

  Spencer Passmore

  committed
  8c3672c

Commits on Mar 17, 2024

• Resolved missed stashed changes

  Phoelionix

  committed
  055851b

• Small misc changes to damage landscape plotting data handling

  Phoelionix

  committed
  52f6c0a

• Fixed foolish mistake of unlocking all electron shells for calculation.

  Phoelionix

  committed
  04fbe0b

Commits on Mar 19, 2024

• critical todo for fixing issue introduced by last commit

  Phoelionix

  committed
  f1167b1

Commits on Mar 21, 2024

• Fixed issue where program would attempt to load forbidden configurations.

  Show description for 9d8159b
  Phoelionix

  committed
  9d8159b

• Misc changes for merging with HPC

  Phoelionix

  committed
  ef3beae

• Suspicions were correct. Now generates separate decay rate files for each set of allowed configs. Also flagged that the implementation of multiple energies wasn't properly accounting for this.

  Phoelionix

  committed
  e56282b

Commits on Mar 22, 2024

• Removed assertion that was misunderstanding the code's logic

  Phoelionix

  committed
  dfc26f5

Commits on Mar 27, 2024

• syncing scripts and new inputs

  Phoelionix

  committed
  5a78262

Commits on Apr 3, 2024

• misc sync changes

  Phoelionix

  committed
  35fa100

Commits on Apr 5, 2024

• Buggy implementation of split eii

  Phoelionix

  committed
  29b72ce

Commits on Apr 6, 2024

• update period now independent of early cutoff time.

  Phoelionix

  committed
  301a96b

• Continuing to work on bugs for split continuum, plotter_core.py updated scrappily to allow for combining cascade continuums (e.g. CNO)

  Phoelionix

  committed
  d1e2bc9

Commits on Aug 23, 2024

• sync

  Phoelionix

  committed
  a68d2c8

• sync2

  Phoelionix

  committed
  b550073

• Got split continuum working. Now tracks cascades spawned by each element.

  Phoelionix

  committed
  f44a530

Commits on Sep 14, 2024

• Fixed graphing 2 subplots + y axis starts at 0 by default for element charge plot

  Phoelionix

  committed
  6cf2dea

• Added (very rough) I3C inputs

  Phoelionix

  committed
  706dd14

• Merge pull request #8 from Phoelionix/split_eii

  Show description for 3cbd97d
  Phoelionix

  authored
  3cbd97d

• Update README.md

  Phoelionix

  authored
  4de3812

Commits on Dec 7, 2024

• Updated config file to make program more generally compatible

  Phoelionix

  committed
  662bd14