v2.5.2

src/acom_music_box/__init__.py

@@ -4,7 +4,7 @@
 This package contains modules for handling various aspects of a music box,
 including species, products, reactants, reactions, and more.
 """
-__version__ = "2.5.1"
+__version__ = "2.5.2"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 from .species import Species

src/acom_music_box/conditions.py

@@ -1,4 +1,4 @@
-from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
+from .utils import convert_pressure, convert_temperature, convert_concentration
 from .species_concentration import SpeciesConcentration
 from .species import Species
 from .reaction_rate import ReactionRate
@@ -9,7 +9,6 @@
 from .reaction_rate import ReactionRate
 from .species import Species
 from .species_concentration import SpeciesConcentration
-from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 
 import logging
 logger = logging.getLogger(__name__)
@@ -54,7 +53,7 @@ def __str__(self):
         return f"Pressure: {self.pressure}, Temperature: {self.temperature}, Species Concentrations: {self.species_concentrations}, Reaction Rates: {self.reaction_rates}"
 
     @classmethod
-    def from_UI_JSON(cls, UI_JSON, species_list, reaction_list):
+    def from_UI_JSON(self, UI_JSON, species_list, reaction_list):
         """
         Creates an instance of the class from a UI JSON object.
 
@@ -108,15 +107,15 @@ def from_UI_JSON(cls, UI_JSON, species_list, reaction_list):
 
             reaction_rates.append(ReactionRate(reaction_from_list, rate))
 
-        return cls(
+        return self(
             pressure,
             temperature,
             species_concentrations,
             reaction_rates)
 
     @classmethod
     def from_config_JSON(
-            cls,
+            self,
             path_to_json,
             config_JSON,
             species_list,
@@ -164,7 +163,7 @@ def from_config_JSON(
             for chem_spec in config_JSON['chemical species']:
                 species = Species(name=chem_spec)
                 concentration = convert_concentration(
-                    config_JSON['chemical species'][chem_spec], 'initial value')
+                    config_JSON['chemical species'][chem_spec], 'initial value', temperature, pressure)
 
                 species_concentrations.append(
                     SpeciesConcentration(
@@ -190,14 +189,14 @@ def from_config_JSON(
             if not reaction_exists:
                 reaction_rates.append(ReactionRate(reaction, 0))
 
-        return cls(
+        return self(
             pressure,
             temperature,
             species_concentrations,
             reaction_rates)
 
     @classmethod
-    def read_initial_rates_from_file(cls, file_path, reaction_list):
+    def read_initial_rates_from_file(self, file_path, reaction_list):
         """
         Reads initial reaction rates from a file.
 

src/acom_music_box/constants.py

@@ -1,3 +1,3 @@
-BOLTZMANN_CONSTANT = 1.380649e-23
-AVOGADRO_CONSTANT = 6.02214076e23
-GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT
+BOLTZMANN_CONSTANT = 1.380649e-23       # joules / Kelvin
+AVOGADRO_CONSTANT = 6.02214076e23       # / mole
+GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT   # joules / Kelvin-mole

src/acom_music_box/examples/configs/analytical/my_config.json

@@ -26,7 +26,6 @@
     }
   },
   "evolving conditions": {
-    "evolving_conditions.csv": {}
   },
   "initial conditions": {},
   "model components": [

src/acom_music_box/music_box.py

@@ -10,7 +10,6 @@
 import pandas as pd
 
 from tqdm import tqdm
-from tqdm.contrib.logging import logging_redirect_tqdm
 
 import logging
 logger = logging.getLogger(__name__)
@@ -55,7 +54,6 @@ def __init__(
         self.evolving_conditions = evolving_conditions if evolving_conditions is not None else EvolvingConditions([
         ], [])
         self.config_file = config_file if config_file is not None else "camp_data/config.json"
-
         self.solver = None
 
     def add_evolving_condition(self, time_point, conditions):
@@ -70,26 +68,6 @@ def add_evolving_condition(self, time_point, conditions):
             time=[time_point], conditions=[conditions])
         self.evolvingConditions.append(evolving_condition)
 
-    def create_solver(
-            self,
-            path_to_config,
-            solver_type=musica.micmsolver.rosenbrock,
-            number_of_grid_cells=1):
-        """
-        Creates a micm solver object using the CAMP configuration files.
-
-        Args:
-            path_to_config (str): The path to CAMP configuration directory.
-
-        Returns:
-            None
-        """
-        # Create a solver object using the configuration file
-        self.solver = musica.create_solver(
-            path_to_config,
-            solver_type,
-            number_of_grid_cells)
-
     def check_config(self, boxConfigPath):
         """
         Verifies correct configuration of the MusicBox object.
@@ -106,7 +84,17 @@ def check_config(self, boxConfigPath):
             Throws error for the first check failed.
         """
 
-        # look for duplicate reaction names
+        # Check for duplicate reactions in the reaction list
+        if self.reaction_list:
+            reaction_names = [reaction.name for reaction in self.reaction_list.reactions]
+            reaction_names = [name for name in reaction_names if name is not None]
+            dup_names = [name for name in reaction_names if reaction_names.count(name) > 1]
+
+            if dup_names:
+                raise Exception(f"Error: Duplicate reaction names specified within {boxConfigPath}: {dup_names}. "
+                                "Please remove or rename the duplicates.")
+
+        # look for duplicate reaction names in the initial conditions
         if (self.initial_conditions):
             if (self.initial_conditions.reaction_rates):
                 reactionNames = []
@@ -301,6 +289,7 @@ def loadJson(self, path_to_json):
 
         with open(path_to_json, 'r') as json_file:
             data = json.load(json_file)
+            self.config_file = data['model components'][0]['configuration file']
             # Set box model options
             self.box_model_options = BoxModelOptions.from_config_JSON(data)
 

src/acom_music_box/reaction_list.py

@@ -81,8 +81,7 @@ def from_config_JSON(cls, path_to_json, config_JSON, species_list):
 
             # assumes reactions file is second in the list
             if (len(config['camp-files']) > 1):
-                reaction_file_path = os.path.dirname(
-                    config_file_path) + "/" + config['camp-files'][1]
+                reaction_file_path = os.path.join(os.path.dirname(config_file_path), config['camp-files'][1])
                 with open(reaction_file_path, 'r') as reaction_file:
                     reaction_data = json.load(reaction_file)
 

src/acom_music_box/species_list.py

@@ -80,8 +80,7 @@ def from_config_JSON(cls, path_to_json, config_JSON):
 
             # assumes species file is first in the list
             if (len(config['camp-files']) > 0):
-                species_file_path = os.path.dirname(
-                    config_file_path) + "/" + config['camp-files'][0]
+                species_file_path = os.path.join(os.path.dirname(config_file_path), config['camp-files'][0])
                 with open(species_file_path, 'r') as species_file:
                     species_data = json.load(species_file)
                     # loads species by names from camp files

src/acom_music_box/tools/waccmToMusicBox.py

@@ -17,6 +17,7 @@
 import tempfile
 import zipfile
 from acom_music_box import Examples
+from acom_music_box.utils import calculate_air_density
 
 import logging
 logger = logging.getLogger(__name__)
@@ -219,19 +220,6 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
     return (musicaDict)
 
 
-# Calculate air density from the ideal gas law.
-# tempK = temperature in degrees Kelvin
-# pressPa = pressure in Pascals
-# return density of air in moles / cubic meter
-def calcAirDensity(tempK, pressPa):
-    BOLTZMANN_CONSTANT = 1.380649e-23       # joules / Kelvin
-    AVOGADRO_CONSTANT = 6.02214076e23       # / mole
-    GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT   # joules / Kelvin-mole
-    airDensity = pressPa / (GAS_CONSTANT * tempK)           # moles / m3
-
-    return airDensity
-
-
 # set up indexes for the tuple
 musicaIndex = 0
 valueIndex = 1
@@ -252,7 +240,7 @@ def convertWaccm(varDict):
     temperature = varDict["temperature"][valueIndex]
     pressure = varDict["pressure"][valueIndex]
     logger.info(f"temperature = {temperature} K   pressure = {pressure} Pa")
-    air_density = calcAirDensity(temperature, pressure)
+    air_density = calculate_air_density(temperature, pressure)
     logger.info(f"air density = {air_density} mol m-3")
 
     for key, vTuple in varDict.items():