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updating to most recent musica version #298

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merged 3 commits into from
Jan 6, 2025
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Merged

updating to most recent musica version #298

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bbfc999
updating to most recent musica version
K20shores Dec 20, 2024
41aa457
updating version in citation file
K20shores Dec 20, 2024
d4cc51a
adding contributor
K20shores Dec 20, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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Expand Up @@ -21,7 +21,7 @@ classifiers = ["License :: OSI Approved :: Apache Software License"]
dynamic = ["version", "description"]

dependencies = [
"musica==0.8.1",
"musica==0.9.0",
"xarray",
"colorlog",
"pandas",
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2 changes: 1 addition & 1 deletion src/acom_music_box/__init__.py
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Expand Up @@ -4,7 +4,7 @@
This package contains modules for handling various aspects of a music box,
including species, products, reactants, reactions, and more.
"""
__version__ = "2.5.5"
__version__ = "2.6.0"

from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
from .model_options import BoxModelOptions
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5 changes: 2 additions & 3 deletions src/acom_music_box/music_box.py
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Expand Up @@ -154,8 +154,7 @@ def solve(self, callback=None):
next_conditions = None

# calculate air density from the ideal gas law
air_density = curr_conditions.pressure / \
(GAS_CONSTANT * curr_conditions.temperature)
air_density = curr_conditions.pressure / (GAS_CONSTANT * curr_conditions.temperature)

# outputs to output_array if enough time has elapsed
if (next_output_time <= curr_time):
Expand Down Expand Up @@ -229,7 +228,7 @@ def loadJson(self, path_to_json):
camp_path = os.path.join(os.path.dirname(path_to_json), self.config_file)

# Initalize the musica solver
self.solver = musica.create_solver(camp_path, musica.micmsolver.rosenbrock, 1)
self.solver = musica.create_solver(camp_path, musica.micmsolver.rosenbrock_standard_order, 1)
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Just curious, why has the solver type changed?

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The vector ordered solver has a default vector lenght of 4. It is the callers responsibility to appropriately size the input array to match what musica expects to write the results to. In this case, musica blindly copies the output values

https://github.com/NCAR/musica/blob/1debffba28d0601cbd646e475cd6751d06e5a8b3/src/micm/micm.cpp#L464-L465

So, if we have only 1 grid cell and 2 species, micm would internally hold a state array of length 8 (species 1 cell 1, specie 1 cell 2, specie 1 cell 3, species 1, cell 4, species 2 cell 1, species 2 cell 2, species 3 cell 3, species 4 cell 4). Thus, music box would need to correctly calculate the size of this array.

It's easiest to use the standard ordered solver because we don't have to care about those empty cells

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Ah, thank you for the detailed explanation!


@staticmethod
def order_reaction_rates(curr_conditions, rate_constant_ordering):
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