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Fix csvy density#2483

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wkerzendorf wants to merge 65 commits intotardis-sn:mastertardis-sn/tardis:masterfrom wkerzendorf:fix_csvy_densitywkerzendorf/tardis:fix_csvy_densityCopy head branch name to clipboard

+1,084-704

Commits

Commits on Sep 28, 2023

• restructure of geometry

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  314cf30

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Commits on Oct 4, 2023

• add radial1d boundary logic

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  d353133

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• black format

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  2475551

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• several fixes

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  e6d1697

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• fix epsilon

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  3c53cda

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• add testing of boundaries

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  6dce2b4

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• change the r_inner_active

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  1fdcea8

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Commits on Oct 7, 2023

• first integration with from_config working

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  56e9da5

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Commits on Oct 8, 2023

• hunting down density indexing bug

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  f6743d7

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• all model tests (without csvy) pass

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  b55b21d

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Commits on Oct 9, 2023

• more fixes

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  ed978d9

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• fix of model to simulation_state

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  cae9c19

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• fix inner boundary packet error

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  d829e73

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Commits on Oct 10, 2023

• fix some leftovers

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  9592a97

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• final fix for csvy

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  committed
  4da6869

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• blackify

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  f381d2e

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Commits on Oct 11, 2023

• restructure to readers and remove some leftover code

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  committed
  e59741d

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• further cleanup

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  a42dd55

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• first start of the restructure

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  committed
  3288c6c

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• add comment about removing quantitiness

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  518a8f9

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• add velocity check

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Commits on Oct 12, 2023

• add new abundance functions

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  006ca9d

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• remove default units

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  committed
  9c680a8

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• add new matter module

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  committed
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• several restructures. move decay from io to tardis/model/matter

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  committed
  6b03e93

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Commits on Oct 13, 2023

• mid restructure

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  3114413

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Commits on Oct 20, 2023

• slow progress on abundance refactor

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  committed
  217dcf2

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Commits on Oct 22, 2023

• include effective_element_masses

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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  73f5175

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Commits on Nov 2, 2023

• further updates

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  b96d717

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• fix of csvy readers

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  committed
  08ea21d

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Commits on Nov 4, 2023

• last fixes to custom abundance widget

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  committed
  f0fc7c2

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Commits on Nov 5, 2023

• some cleanup

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  committed
  226fb57

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• further cleanup

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  committed
  daf12a5

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Commits on Nov 8, 2023

• removing matter

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  4a77a4a

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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  dbd47cc

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Commits on Nov 20, 2023

• fixed last tests

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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  committed
  c757848

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• add composition

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  ed60c0f

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• remove isotopemassfractions

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  8723fdf

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• some small fixes

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  08874ca

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Commits on Nov 21, 2023

• add the from_config atom_data

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  committed
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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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  committed
  4f4aad6

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• fixing model.ipynb

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  f65a2d7

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Commits on Nov 23, 2023

• fix tests

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  committed
  1c38607

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• fix some of the issues wdigets

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  committed
  c99e9d4

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• assert mass fractions positive.

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Commits on Nov 27, 2023

• Fix isotope mass fraction typo and t_radiatve duplicate definition

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  fcd34bb

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• Document remove functionality for effective element masses

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  committed
  1e3a035

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• Fix variable name in

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• Refactor test names and variable names in

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• Merge remote-tracking branch 'upstream/master' into restructure/abundance

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  committed
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Commits on Nov 29, 2023

• Refactor gamma ray simulation setup and test

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  2a50667

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• fix gamma ray tests

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  committed
  b17b7c7

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• Add model_isotope_time_0 property to abundances

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• Refactor config_reader and config_validator

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• Fix model_isotope_time_0 property in

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  e56ddcc

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• Refactor simulation module to use pathlib

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  29fa091

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• remove bad comment and refactor with ruff

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  committed
  8dff14e

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• Fix variable name in test_simulation_state_mass()

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  fcb5dba

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• Fix unit conversion in calculate_cell_masses

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  7da18f3

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• Fix logger debug message in CSV reader and update

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  1bb7266

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• black formatting

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  821f4ce

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• Refactor code to use composition variable in

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  2257093

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• Remove 0-th shell from density array in CSVY case

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