Merge pull request #250 from NCAR/main

v2.5.1

.gitignore

@@ -7,4 +7,6 @@ doc/latex/
 data/
 __pycache__/
 *.pyc
-dist
+dist
+
+.vscode/

pyproject.toml

@@ -21,7 +21,7 @@ classifiers = ["License :: OSI Approved :: Apache Software License"]
 dynamic = ["version", "description"]
 
 dependencies = [
-  "musica==0.8.0",
+  "musica==0.8.1",
   "xarray",
   "colorlog",
   "pandas",

src/acom_music_box/__init__.py

@@ -1,10 +1,10 @@
 """
-This is the music_box package.
+An atmospheric chemistry box model. Powered by MUSICA.
 
 This package contains modules for handling various aspects of a music box,
 including species, products, reactants, reactions, and more.
 """
-__version__ = "2.5.0"
+__version__ = "2.5.1"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 from .species import Species

src/acom_music_box/constants.py

@@ -0,0 +1,3 @@
+BOLTZMANN_CONSTANT = 1.380649e-23
+AVOGADRO_CONSTANT = 6.02214076e23
+GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT

src/acom_music_box/music_box.py

@@ -4,6 +4,7 @@
 from .species_list import SpeciesList
 from .reaction_list import ReactionList
 from .evolving_conditions import EvolvingConditions
+from .constants import GAS_CONSTANT
 import json
 import os
 import pandas as pd
@@ -221,9 +222,6 @@ def solve(self, output_path=None, callback=None):
                         next_conditions = None
 
                 #  calculate air density from the ideal gas law
-                BOLTZMANN_CONSTANT = 1.380649e-23
-                AVOGADRO_CONSTANT = 6.02214076e23
-                GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT
                 air_density = curr_conditions.pressure / \
                     (GAS_CONSTANT * curr_conditions.temperature)
 
@@ -333,18 +331,6 @@ def loadJson(self, path_to_json):
             musica.micmsolver.rosenbrock,
             1)
 
-    def speciesOrdering(self):
-        """
-        Retrieves the ordering of species used in the solver.
-
-        This function calls the `species_ordering` function from the `musica` module,
-        passing the solver instance from the current object.
-
-        Returns:
-            dict: The ordered dictionary of species used in the solver.
-        """
-        return musica.species_ordering(self.solver)
-
     @classmethod
     def order_reaction_rates(self, curr_conditions, rate_constant_ordering):
         """