Code

Restructure/transport solver#2476

Code

Merged

wkerzendorf merged 165 commits intotardis-sn:mastertardis-sn/tardis:masterfrom wkerzendorf:restructure/transport_solverwkerzendorf/tardis:restructure/transport_solverCopy head branch name to clipboardJan 17, 2024

+1,116-1,634

Commits

Commits on Sep 28, 2023

• restructure of geometry

  wkerzendorf

  committed
  314cf30

  Copy full SHA for 314cf30

Commits on Oct 4, 2023

• add radial1d boundary logic

  wkerzendorf

  committed
  d353133

  Copy full SHA for d353133

• black format

  wkerzendorf

  committed
  2475551

  Copy full SHA for 2475551

• several fixes

  wkerzendorf

  committed
  e6d1697

  Copy full SHA for e6d1697

• fix epsilon

  wkerzendorf

  committed
  3c53cda

  Copy full SHA for 3c53cda

• add testing of boundaries

  wkerzendorf

  committed
  6dce2b4

  Copy full SHA for 6dce2b4

• change the r_inner_active

  wkerzendorf

  committed
  1fdcea8

  Copy full SHA for 1fdcea8

Commits on Oct 7, 2023

• first integration with from_config working

  wkerzendorf

  committed
  56e9da5

  Copy full SHA for 56e9da5

Commits on Oct 8, 2023

• hunting down density indexing bug

  wkerzendorf

  committed
  f6743d7

  Copy full SHA for f6743d7

• all model tests (without csvy) pass

  wkerzendorf

  committed
  b55b21d

  Copy full SHA for b55b21d

Commits on Oct 9, 2023

• more fixes

  wkerzendorf

  committed
  ed978d9

  Copy full SHA for ed978d9

• fix of model to simulation_state

  wkerzendorf

  committed
  cae9c19

  Copy full SHA for cae9c19

• fix inner boundary packet error

  wkerzendorf

  committed
  d829e73

  Copy full SHA for d829e73

Commits on Oct 10, 2023

• fix some leftovers

  wkerzendorf

  committed
  9592a97

  Copy full SHA for 9592a97

• final fix for csvy

  wkerzendorf

  committed
  4da6869

  Copy full SHA for 4da6869

• blackify

  wkerzendorf

  committed
  f381d2e

  Copy full SHA for f381d2e

Commits on Oct 11, 2023

• restructure to readers and remove some leftover code

  wkerzendorf

  committed
  e59741d

  Copy full SHA for e59741d

• further cleanup

  wkerzendorf

  committed
  a42dd55

  Copy full SHA for a42dd55

• first start of the restructure

  wkerzendorf

  committed
  3288c6c

  Copy full SHA for 3288c6c

• add comment about removing quantitiness

  wkerzendorf

  committed
  518a8f9

  Copy full SHA for 518a8f9

• add velocity check

  wkerzendorf

  committed
  c78b6de

  Copy full SHA for c78b6de

Commits on Oct 12, 2023

• add new abundance functions

  wkerzendorf

  committed
  006ca9d

  Copy full SHA for 006ca9d

• remove default units

  wkerzendorf

  committed
  9c680a8

  Copy full SHA for 9c680a8

• add new matter module

  wkerzendorf

  committed
  268bd23

  Copy full SHA for 268bd23

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

  wkerzendorf

  committed
  6b03e93

  Copy full SHA for 6b03e93

Commits on Oct 13, 2023

• mid restructure

  wkerzendorf

  committed
  3114413

  Copy full SHA for 3114413

Commits on Oct 20, 2023

• slow progress on abundance refactor

  wkerzendorf

  committed
  217dcf2

  Copy full SHA for 217dcf2

Commits on Oct 22, 2023

• include effective_element_masses

  wkerzendorf

  committed
  78055b4

  Copy full SHA for 78055b4

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

  wkerzendorf

  committed
  73f5175

  Copy full SHA for 73f5175

Commits on Nov 2, 2023

• further updates

  wkerzendorf

  committed
  b96d717

  Copy full SHA for b96d717

• fix of csvy readers

  wkerzendorf

  committed
  08ea21d

  Copy full SHA for 08ea21d

Commits on Nov 4, 2023

• last fixes to custom abundance widget

  wkerzendorf

  committed
  f0fc7c2

  Copy full SHA for f0fc7c2

Commits on Nov 5, 2023

• restructuring the radiation field

  wkerzendorf

  committed
  fe7c415

  Copy full SHA for fe7c415

• some cleanup

  wkerzendorf

  committed
  226fb57

  Copy full SHA for 226fb57

• Merge branch 'restructure/abundance' into restructure/radiation_field

  wkerzendorf

  committed
  cbd025e

  Copy full SHA for cbd025e

• cleanup

  wkerzendorf

  committed
  afb9613

  Copy full SHA for afb9613

• further cleanup

  wkerzendorf

  committed
  daf12a5

  Copy full SHA for daf12a5

• Merge branch 'restructure/abundance' into restructure/radiation_field

  wkerzendorf

  committed
  f2d26a8

  Copy full SHA for f2d26a8

• clearnup

  wkerzendorf

  committed
  7575512

  Copy full SHA for 7575512

Commits on Nov 6, 2023

• changes

  wkerzendorf

  committed
  dc34343

  Copy full SHA for dc34343

Commits on Nov 8, 2023

• remove matter base.py

  wkerzendorf

  committed
  37d36e1

  Copy full SHA for 37d36e1

• removing matter

  wkerzendorf

  committed
  4a77a4a

  Copy full SHA for 4a77a4a

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

  wkerzendorf

  committed
  dbd47cc

  Copy full SHA for dbd47cc

Commits on Nov 20, 2023

• fixed last tests

  wkerzendorf

  committed
  d1792bf

  Copy full SHA for d1792bf

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

  wkerzendorf

  committed
  c757848

  Copy full SHA for c757848

• first commit for regression_data

  wkerzendorf

  committed
  1f42760

  Copy full SHA for 1f42760

• Merge branch 'restructure/abundance' into restructure/radiation_field

  wkerzendorf

  committed
  5b1c7b2

  Copy full SHA for 5b1c7b2

• add several parsers

  wkerzendorf

  committed
  398631a

  Copy full SHA for 398631a

• add composition

  wkerzendorf

  committed
  ed60c0f

  Copy full SHA for ed60c0f

• remove isotopemassfractions

  wkerzendorf

  committed
  8723fdf

  Copy full SHA for 8723fdf

• some small fixes

  wkerzendorf

  committed
  08874ca

  Copy full SHA for 08874ca

• Merge branch 'restructure/abundance' into restructure/radiation_field

  wkerzendorf

  committed
  d89b957

  Copy full SHA for d89b957

• fixed w, t_rad to dilution_factor, t_radiative

  wkerzendorf

  committed
  1da7ed0

  Copy full SHA for 1da7ed0

• add setters for w, t_rad

  wkerzendorf

  committed
  9f28ecd

  Copy full SHA for 9f28ecd

Commits on Nov 21, 2023

• several fixes for instantiating the right t_rads.

  Show description for 0d85540
  wkerzendorf

  committed
  0d85540

  Copy full SHA for 0d85540

• add the from_config atom_data

  wkerzendorf

  committed
  7161791

  Copy full SHA for 7161791

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

  wkerzendorf

  committed
  4f4aad6

  Copy full SHA for 4f4aad6

• fixing model.ipynb

  wkerzendorf

  committed
  f65a2d7

  Copy full SHA for f65a2d7

• Merge branch 'restructure/abundance' into restructure/radiation_field

  wkerzendorf

  committed
  cbfe685

  Copy full SHA for cbfe685

• fix some more tests

  wkerzendorf

  committed
  b961734

  Copy full SHA for b961734

• start of montecarlo restructure

  wkerzendorf

  committed
  63a86fb

  Copy full SHA for 63a86fb

Commits on Nov 22, 2023

• large scale changes

  wkerzendorf

  committed
  1d46d45

  Copy full SHA for 1d46d45

Commits on Nov 23, 2023

• further disentangling state and solver

  wkerzendorf

  committed
  9a21714

  Copy full SHA for 9a21714

• fix tests

  wkerzendorf

  committed
  1c38607

  Copy full SHA for 1c38607

• fix some of the issues wdigets

  wkerzendorf

  committed
  c99e9d4

  Copy full SHA for c99e9d4

• assert mass fractions positive.

  Show description for 4c0b49a
  wkerzendorf

  committed
  4c0b49a

  Copy full SHA for 4c0b49a

• update estimators

  wkerzendorf

  committed
  7474e66

  Copy full SHA for 7474e66

• add packet collection

  wkerzendorf

  committed
  6735fad

  Copy full SHA for 6735fad

• move spectrum to mct_state

  wkerzendorf

  committed
  2135c5a

  Copy full SHA for 2135c5a

• add radiation_field_state

  wkerzendorf

  committed
  8e0de5c

  Copy full SHA for 8e0de5c

• Merge branch 'restructure/radiation_field' into restructure/transport_solver

  wkerzendorf

  committed
  ba9cdf6

  Copy full SHA for ba9cdf6

Commits on Nov 24, 2023

• Refactor packet initialization in

  Show description for 8fd5633
  wkerzendorf

  committed
  8fd5633

  Copy full SHA for 8fd5633

• Update model_nparray_attrs in test_base.py and fix

  Show description for 305e89d
  wkerzendorf

  committed
  305e89d

  Copy full SHA for 305e89d

• Fix temperature assertion in

  Show description for de63d0f
  wkerzendorf

  committed
  de63d0f

  Copy full SHA for de63d0f

Commits on Nov 26, 2023

• Fix Integrator

  wkerzendorf

  committed
  0f4608a

  Copy full SHA for 0f4608a

• Fix SDEC plot for MCTState

  wkerzendorf

  committed
  098cc76

  Copy full SHA for 098cc76

• Fix variable names in transport module

  wkerzendorf

  committed
  455a820

  Copy full SHA for 455a820

Commits on Nov 27, 2023

• Refactor the to_hdf code.

  wkerzendorf

  committed
  9de8b34

  Copy full SHA for 9de8b34

• Fix isotope mass fraction typo and t_radiatve duplicate definition

  wkerzendorf

  committed
  fcd34bb

  Copy full SHA for fcd34bb

• Document remove functionality for effective element masses

  wkerzendorf

  committed
  1e3a035

  Copy full SHA for 1e3a035

• Fix variable name in

  Show description for af1f114
  wkerzendorf

  committed
  af1f114

  Copy full SHA for af1f114

• Refactor test names and variable names in

  Show description for 203bae0
  wkerzendorf

  committed
  203bae0

  Copy full SHA for 203bae0

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

  wkerzendorf

  committed
  56aaa8c

  Copy full SHA for 56aaa8c

Commits on Nov 29, 2023

• Refactor gamma ray simulation setup and test

  Show description for 2a50667
  wkerzendorf

  committed
  2a50667

  Copy full SHA for 2a50667

• fix gamma ray tests

  wkerzendorf

  committed
  b17b7c7

  Copy full SHA for b17b7c7

• Add model_isotope_time_0 property to abundances

  Show description for a479cf6
  wkerzendorf

  committed
  a479cf6

  Copy full SHA for a479cf6

• Add test for montecarlo main loop with vpacket

  Show description for 6d64b2d
  wkerzendorf

  committed
  6d64b2d

  Copy full SHA for 6d64b2d

• Refactor config_reader and config_validator

  Show description for b92158d
  wkerzendorf

  committed
  b92158d

  Copy full SHA for b92158d

• Fix model_isotope_time_0 property in

  Show description for e56ddcc
  wkerzendorf

  committed
  e56ddcc

  Copy full SHA for e56ddcc

• Refactor simulation module to use pathlib

  wkerzendorf

  committed
  29fa091

  Copy full SHA for 29fa091

• remove bad comment and refactor with ruff

  wkerzendorf

  committed
  8dff14e

  Copy full SHA for 8dff14e

• Fix variable name in test_simulation_state_mass()

  Show description for fcb5dba
  wkerzendorf

  committed
  fcb5dba

  Copy full SHA for fcb5dba

• Fix unit conversion in calculate_cell_masses

  Show description for 7da18f3
  wkerzendorf

  committed
  7da18f3

  Copy full SHA for 7da18f3

• Fix logger debug message in CSV reader and update

  Show description for 1bb7266
  wkerzendorf

  committed
  1bb7266

  Copy full SHA for 1bb7266

• black formatting

  wkerzendorf

  committed
  821f4ce

  Copy full SHA for 821f4ce

• Refactor code to use composition variable in

  Show description for 2257093
  wkerzendorf

  committed
  2257093

  Copy full SHA for 2257093

Commits on Nov 30, 2023

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

  wkerzendorf

  committed
  e105e71

  Copy full SHA for e105e71

• Refactor imports in atom_web_download.py and

  Show description for 75840d3
  wkerzendorf

  committed
  75840d3

  Copy full SHA for 75840d3

Commits on Dec 4, 2023

• fix for documentation not builiding

  wkerzendorf

  committed
  59d5eff

  Copy full SHA for 59d5eff

• add fix for model_isotope_time_0

  wkerzendorf

  committed
  1f65771

  Copy full SHA for 1f65771

• fix grid test

  wkerzendorf

  committed
  dd6ba4f

  Copy full SHA for dd6ba4f

• restructure the grid

  wkerzendorf

  committed
  5391968

  Copy full SHA for 5391968

• final change

  wkerzendorf

  committed
  9706437

  Copy full SHA for 9706437

• Merge branch 'restructure/abundance' into restructure/radiation_field

  wkerzendorf

  committed
  512d737

  Copy full SHA for 512d737

• add stuff

  wkerzendorf

  committed
  c6d3a59

  Copy full SHA for c6d3a59

• add vpacket_log

  wkerzendorf

  committed
  d9a191c

  Copy full SHA for d9a191c

• Refactor model_reader.py and shell_info.py

  Show description for b31561e
  wkerzendorf

  committed
  b31561e

  Copy full SHA for b31561e

• Update damping constants and variable names

  Show description for f438ec3
  wkerzendorf

  committed
  f438ec3

  Copy full SHA for f438ec3

• fix w in several places in tardis

  wkerzendorf

  committed
  ef8cf30

  Copy full SHA for ef8cf30

• slowly fixing radiation_field changes

  wkerzendorf

  committed
  361e0b7

  Copy full SHA for 361e0b7

• Merge remote-tracking branch 'origin/restructure/radiation_field' into restructure/radiation_field

  wkerzendorf

  committed
  d5cb35d

  Copy full SHA for d5cb35d

• last fix

  wkerzendorf

  committed
  6244535

  Copy full SHA for 6244535

• change hdf from model to simulation_state

  wkerzendorf

  committed
  3c8f3da

  Copy full SHA for 3c8f3da

• fixing model->simulation-state

  wkerzendorf

  committed
  815b0d8

  Copy full SHA for 815b0d8

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

  wkerzendorf

  committed
  5925f6e

  Copy full SHA for 5925f6e

• Fix model_reader.py imports and formatting issues

  wkerzendorf

  committed
  81ebd21

  Copy full SHA for 81ebd21

• Refactor variable names for clarity and

  Show description for e24f1fa
  wkerzendorf

  committed
  e24f1fa

  Copy full SHA for e24f1fa

• Update variable names in model.ipynb

  wkerzendorf

  committed
  50d3ec3

  Copy full SHA for 50d3ec3

• Update variable name for average temperature

  Show description for 566d279
  wkerzendorf

  committed
  566d279

  Copy full SHA for 566d279

Commits on Dec 5, 2023

• Merge branch 'restructure/radiation_field' into restructure/transport_solver

  wkerzendorf

  committed
  f068e64

  Copy full SHA for f068e64

• Fix file paths in test_grid.py, test_base.py,

  Show description for 86a4974
  wkerzendorf

  committed
  86a4974

  Copy full SHA for 86a4974

• Fix transport dictionary comparison

  wkerzendorf

  committed
  145a9fc

  Copy full SHA for 145a9fc

Commits on Dec 7, 2023

• Merge branch 'restructure/radiation_field' into tests/regression_data

  wkerzendorf

  committed
  871b849

  Copy full SHA for 871b849

Commits on Dec 9, 2023

• Implement regression data configurations

  wkerzendorf

  committed
  eb0e055

  Copy full SHA for eb0e055

• Refactor snapshot fixtures and add regression data

  Show description for d0c26dd
  wkerzendorf

  committed
  d0c26dd

  Copy full SHA for d0c26dd

Commits on Dec 10, 2023

• Update to new testing framework

  wkerzendorf

  committed
  67236a4

  Copy full SHA for 67236a4

• Merge remote-tracking branch 'origin/restructure/radiation_field' into tests/regression_data

  wkerzendorf

  committed
  5e04422

  Copy full SHA for 5e04422

• Refactor imports and fixtures in conftest.py and

  Show description for e18bfe0
  wkerzendorf

  committed
  e18bfe0

  Copy full SHA for e18bfe0

• Make regression-data optional

  wkerzendorf

  committed
  a68a006

  Copy full SHA for a68a006

• Fix regression data synchronization in plasma

  Show description for f219356
  wkerzendorf

  committed
  f219356

  Copy full SHA for f219356

• Refactor variable names in model reader and

  Show description for a949f49
  wkerzendorf

  committed
  a949f49

  Copy full SHA for a949f49

• Refactor store_model_to_hdf to

  Show description for 56a948d
  wkerzendorf

  committed
  56a948d

  Copy full SHA for 56a948d

Commits on Dec 11, 2023

• Refactor HDF file handling and model reader

  Show description for 2e6caac
  wkerzendorf

  committed
  2e6caac

  Copy full SHA for 2e6caac

• add docstr

  wkerzendorf

  committed
  1cc8004

  Copy full SHA for 1cc8004

• Merge branch 'restructure/radiation_field' into tests/regression_data

  wkerzendorf

  committed
  e5dedcc

  Copy full SHA for e5dedcc

• Merge branch 'tests/regression_data' into restructure/transport_solver

  wkerzendorf

  committed
  537e7d3

  Copy full SHA for 537e7d3

• Merge remote-tracking branch 'upstream/master' into tests/regression_data

  wkerzendorf

  committed
  0044907

  Copy full SHA for 0044907

• Remove syrupy_extensions.py

  wkerzendorf

  committed
  f1151c3

  Copy full SHA for f1151c3

Commits on Dec 14, 2023

• Refactor code and remove unused imports and

  Show description for c85d64e
  wkerzendorf

  committed
  c85d64e

  Copy full SHA for c85d64e

Commits on Dec 15, 2023

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

  wkerzendorf

  committed
  dc1cffe

  Copy full SHA for dc1cffe

• Fix test_base and test_simulation

  wkerzendorf

  committed
  5a902a4

  Copy full SHA for 5a902a4

• setting up regression with github actions

  wkerzendorf

  committed
  b0e6eac

  Copy full SHA for b0e6eac

Commits on Dec 16, 2023

• Update LFS cache IDs for refdata and regression

  Show description for 6cc25b7
  wkerzendorf

  committed
  6cc25b7

  Copy full SHA for 6cc25b7

• Fix test_montecarlo_radial1d function

  wkerzendorf

  committed
  ccf0a99

  Copy full SHA for ccf0a99

• Update sync_hdf_store method in RegressionData class

  wkerzendorf

  committed
  71f1317

  Copy full SHA for 71f1317

• Refactor test_base.py for improved accuracy and precision

  wkerzendorf

  committed
  0a1ae4a

  Copy full SHA for 0a1ae4a

• update docstrings

  wkerzendorf

  committed
  74cf7a2

  Copy full SHA for 74cf7a2

• Merge branch 'tests/regression_data' into restructure/transport_solver

  wkerzendorf

  committed
  173b0f0

  Copy full SHA for 173b0f0

Commits on Dec 20, 2023

• Refactor transport state access in test_base.py

  wkerzendorf

  committed
  57d4055

  Copy full SHA for 57d4055

• Fix warnings and add HDF output in sdec_plot.ipynb and cleanup regression_data.py

  wkerzendorf

  committed
  fb09b33

  Copy full SHA for fb09b33

Commits on Dec 21, 2023

• Update demo.hdf file

  Show description for 3e86d61
  wkerzendorf

  committed
  3e86d61

  Copy full SHA for 3e86d61

Commits on Dec 24, 2023

• Fix negative values in last_interaction_types

  wkerzendorf

  committed
  c9c9ee0

  Copy full SHA for c9c9ee0

• Update URL for atomic data repository

  wkerzendorf

  committed
  69e85cf

  Copy full SHA for 69e85cf

• Refactor code for improved readability and maintainability

  wkerzendorf

  committed
  8c7759a

  Copy full SHA for 8c7759a

• Refactor code to remove unnecessary array conversion

  wkerzendorf

  committed
  a0a23a0

  Copy full SHA for a0a23a0

• Refactor code to remove unnecessary conversion to numpy array in test_hdf_scalars

  wkerzendorf

  committed
  5ff5432

  Copy full SHA for 5ff5432

• Merge branch 'tests/regression_data' into restructure/transport_solver

  wkerzendorf

  committed
  16afba3

  Copy full SHA for 16afba3

Commits on Jan 5, 2024

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

  wkerzendorf

  committed
  598de5c

  Copy full SHA for 598de5c

• fixed comments

  wkerzendorf

  committed
  2447542

  Copy full SHA for 2447542

Commits on Jan 13, 2024

• fix some of josh's requests

  wkerzendorf

  committed
  8e0f3a9

  Copy full SHA for 8e0f3a9

Commits on Jan 16, 2024

• Fix callback example doc and parse_packet_source missing import

  andrewfullard

  committed
  45fa00a

  Copy full SHA for 45fa00a

• Fixes custom packet source through init function

  andrewfullard

  committed
  480c52e

  Copy full SHA for 480c52e

• Fixes docs build

  andrewfullard

  committed
  37aca1f

  Copy full SHA for 37aca1f

• black format on parse_input

  andrewfullard

  committed
  bd62bd1

  Copy full SHA for bd62bd1

• Fixes tests for packet source

  Show description for 1e3cb54
  andrewfullard

  committed
  1e3cb54

  Copy full SHA for 1e3cb54