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Python box model #147

Merged
merged 82 commits into from
Apr 9, 2024
Merged

Python box model #147

merged 82 commits into from
Apr 9, 2024

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alexjamesgarza
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@alexjamesgarza alexjamesgarza commented Mar 28, 2024 •
edited by K20shores
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Rewrite MusicBox in python

K20shores and others added 30 commits February 22, 2024 15:26
@K20shores
setting up a cmake structure for c++
c78ab07
@alexjamesgarza
python box model iniital classes
24d93e4
@alexjamesgarza
added method for generating species config
b72c48b
@alexjamesgarza
added relative tolerance to spec config
398d571
@alexjamesgarza
added method to generate reaction config
8edf3b9
@alexjamesgarza
added generateConfig documentation and todo solve function
c421e08
@alexjamesgarza
added todo readfromjson function
55815eb
@alexjamesgarza
added params to reaction
6ad84c8
@alexjamesgarza
updated Reaction and getReactionConfig to handle A B D E and Ea param…
d7e228a 
…aters
@eadlg2
can mostly parse json file from UI
70007b2
@alexjamesgarza
implemented skeleton logic for solver
67a45b0
@eadlg2
extracted concentrations and reaction rates from evolving conditions
a9b0781
@eadlg2
added initial reaction rates, need to verify
3adbc51
@eadlg2
made conversion functions to shorten code
ecbe62a
@eadlg2
tested parsing with example that had every option
f34bd93
@eadlg2
added other reaction types and refactored some code
a1d5370
@eadlg2
fixed bug in species list
cb8a62e
@eadlg2
fixed bug in reaction list
a5fa131
@eadlg2
generateReactionConfig accounts for the different types of reactions
4aea08c
@alexjamesgarza
added funciton to create micm solver based on config
37ac711
@alexjamesgarza
added funciton to create micm solver based on config
156a4d0
@alexjamesgarza
working towards box model test
bbe8d0f
@alexjamesgarza
adds function to read config json and tests basic reaction
74ee215
@alexjamesgarza
fixed solve to inc by seconds
0a4f600
@eadlg2
convert time steps to seconds
e13b7ee
@alexjamesgarza
updated solve with new time units
a2888c4
@alexjamesgarza
Changed readFromJson to readFromUIJosn
2521880
@eadlg2
convert_pressure converts to Pa now
a9dca12
@alexjamesgarza
outputs results to file and creates file for initial test
128528b
@alexjamesgarza
reads species name from config
2819f1f
eadlg2 and others added 25 commits April 2, 2024 13:29
@eadlg2
fixed unit issue with pressure for setting up evolving conditions
a858456
@alexjamesgarza
added reaction type prefixes in order_reaction_ratesz
3e59536
@alexjamesgarza
changed evolving conditions to update in a while loop in case chem ti…
c849c6f 
…me step is greater than time between evolving conditions
@alexjamesgarza
updated python test 3
1facdae
@alexjamesgarza
creates test for chapman in python_test_3.py
2b8bf84
@alexjamesgarza
renamed tests to be more descriptive
8414a38
@alexjamesgarza
added test file for wall-loss
66d2683
@eadlg2
include base values for reactions, change C back to Ea
745d7d5
@eadlg2
Merge branch 'python_box_model' of https://github.com/NCAR/music-box …
dbcbb9f 
…into python_box_model
@eadlg2
add species not present in initial conditions for order_species_conce…
993fbdf 
…ntration
@alexjamesgarza
removed unused files
0ad1d29
@alexjamesgarza
Merge branch 'python_box_model' of https://github.com/NCAR/music-box …
df7d99e 
…into python_box_model
@alexjamesgarza
removed unused files
0db500e
@alexjamesgarza
created .whl for music_box package
81b820b
@eadlg2
make sure time in evolving conditions is float
5315cc0
@eadlg2
check reaction names correctly for evolving conditions config, ensure…
9663de5 
… floats for rate constants
@alexjamesgarza
added function to read from UI json string
b78fafc
@alexjamesgarza
Merge branch 'python_box_model' of https://github.com/NCAR/music-box …
2bcc8bf 
…into python_box_model
@K20shores
removing fortran things, using musica python module, creating install…
9908e61 
…ation suitable for pypi
@K20shores
converting tests to pytest
d290604
@K20shores
correcting setup python?
5e11aa4
@K20shores
adding a space
085e896
@K20shores
strategy
9e50e85
@K20shores
installing music_box in CI
d9820c8
@K20shores
newer checkout
11bf7a4
@K20shores K20shores mentioned this pull request Apr 9, 2024
Closed
@K20shores K20shores merged commit d77109b into main Apr 9, 2024
3 checks passed
@K20shores K20shores deleted the python_box_model branch April 9, 2024 15:46
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@K20shores K20shores K20shores approved these changes

@mattldawson mattldawson Awaiting requested review from mattldawson

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3 participants
@alexjamesgarza @K20shores @eadlg2