Merge branch 'main' into 130-create-musicbox-configuration-for-ts1cap…

…ram-24-reduced-mechanism

.github/workflows/pep8_autoformat.yml

@@ -15,7 +15,7 @@ jobs:
       - name: autopep8
         uses: peter-evans/autopep8@v2
         with:
-          args: --recursive --in-place --aggressive --aggressive --max-line-length 120 .
+          args: --recursive --in-place --aggressive --aggressive --max-line-length 180 .
 
       - name: Check for changes
         id: check-changes

.gitignore

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

CITATION.cff

@@ -1,7 +1,7 @@
 cff-version: 1.2.0
 message: If you use this software, please cite it as below.
 title: MusicBox
-version: v2.1.0
+version: v2.5.0
 authors:
   - family-names: Dawson
     given-names: Matthew

pyproject.toml

@@ -21,7 +21,7 @@ classifiers = ["License :: OSI Approved :: Apache Software License"]
 dynamic = ["version", "description"]
 
 dependencies = [
-  "musica==0.7.3",
+  "musica==0.8.1",
   "xarray",
   "colorlog",
   "pandas",

src/acom_music_box/__init__.py

@@ -1,20 +1,13 @@
 """
-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__ = "2.4.0"
+__version__ = "2.5.3"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
-from .species import Species
-from .product import Product
-from .reactant import Reactant
-from .reaction import Reaction, Branched, Arrhenius, Tunneling, Troe_Ternary
-from .species_list import SpeciesList
 from .model_options import BoxModelOptions
-from .species_concentration import SpeciesConcentration
-from .reaction_rate import ReactionRate
 from .conditions import Conditions
 
 from .evolving_conditions import EvolvingConditions

src/acom_music_box/conditions.py

@@ -1,20 +1,10 @@
-from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
-from .species_concentration import SpeciesConcentration
-from .species import Species
-from .reaction_rate import ReactionRate
-from typing import List
-import csv
+from .utils import convert_pressure, convert_temperature, convert_concentration
+import pandas as pd
 import os
-from typing import List
-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__)
 
-
 class Conditions:
     """
     Represents conditions for a simulation with attributes such as pressure, temperature, species concentrations,
@@ -39,13 +29,13 @@ def __init__(
         Args:
             pressure (float): The pressure of the conditions in atmospheres.
             temperature (float): The temperature of the conditions in Kelvin.
-            species_concentrations (List[SpeciesConcentration]): A list of species concentrations. Default is an empty list.
-            reaction_rates (List[ReactionRate]): A list of reaction rates. Default is an empty list.
+            species_concentrations (Dict[Species, float]): A dictionary of species concentrations.
+            reaction_rates (Dict[Reaction, float]): A dictionary of reaction rates.
         """
         self.pressure = pressure
         self.temperature = temperature
-        self.species_concentrations = species_concentrations if species_concentrations is not None else []
-        self.reaction_rates = reaction_rates if reaction_rates is not None else []
+        self.species_concentrations = species_concentrations if species_concentrations is not None else {}
+        self.reaction_rates = reaction_rates if reaction_rates is not None else {}
 
     def __repr__(self):
         return f"Conditions(pressure={self.pressure}, temperature={self.temperature}, species_concentrations={self.species_concentrations}, reaction_rates={self.reaction_rates})"
@@ -54,7 +44,7 @@ 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.
 
@@ -108,19 +98,17 @@ 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,
-            reaction_list):
+            object):
         """
         Creates an instance of the class from a configuration JSON object.
 
@@ -129,75 +117,51 @@ def from_config_JSON(
 
         Args:
             path_to_json (str): The path to the JSON file containing the initial conditions and settings.
-            config_JSON (dict): The configuration JSON object containing the initial conditions and settings.
-            species_list (SpeciesList): A SpeciesList containing the species involved in the simulation.
-            reaction_list (ReactionList): A ReactionList containing the reactions involved in the simulation.
+            object (dict): The configuration JSON object containing the initial conditions and settings.
 
         Returns:
             object: An instance of the Conditions class with the settings from the configuration JSON object.
         """
         pressure = convert_pressure(
-            config_JSON['environmental conditions']['pressure'],
+            object['environmental conditions']['pressure'],
             'initial value')
 
         temperature = convert_temperature(
-            config_JSON['environmental conditions']['temperature'],
+            object['environmental conditions']['temperature'],
             'initial value')
 
         # Set initial species concentrations
-        species_concentrations = []
-        reaction_rates = []
+        initial_concentrations = {}
+        reaction_rates = {}
 
         # reads initial conditions from csv if it is given
-        if 'initial conditions' in config_JSON and len(
-                list(config_JSON['initial conditions'].keys())) > 0:
+        if 'initial conditions' in object and len(
+                list(object['initial conditions'].keys())) > 0:
 
             initial_conditions_path = os.path.join(
                 os.path.dirname(path_to_json),
-                list(config_JSON['initial conditions'].keys())[0])
+                list(object['initial conditions'].keys())[0])
 
             reaction_rates = Conditions.read_initial_rates_from_file(
-                initial_conditions_path, reaction_list)
+                initial_conditions_path)
 
         # reads from config file directly if present
-        if 'chemical species' in 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')
-
-                species_concentrations.append(
-                    SpeciesConcentration(
-                        species, concentration))
-
-        for species in species_list.species:
-            if species.tracer_type == 'THIRD_BODY':
-                continue
-            if not any(conc.species.name ==
-                       species.name for conc in species_concentrations):
-                species_concentrations.append(SpeciesConcentration(species, 0))
-
-        # Set initial reaction rates
-        for reaction in reaction_list.reactions:
-            if (reaction.name is None):
-                continue
-            reaction_exists = False
-            for rate in reaction_rates:
-                if rate.reaction.name == reaction.name:
-                    reaction_exists = True
-                    break
-
-            if not reaction_exists:
-                reaction_rates.append(ReactionRate(reaction, 0))
-
-        return cls(
+        if 'chemical species' in object:
+            initial_concentrations = {
+                species: convert_concentration(
+                    object['chemical species'][species], 'initial value', temperature, pressure
+                )
+                for species in object['chemical species']
+            }
+
+        return self(
             pressure,
             temperature,
-            species_concentrations,
+            initial_concentrations,
             reaction_rates)
 
     @classmethod
-    def read_initial_rates_from_file(cls, file_path, reaction_list):
+    def read_initial_rates_from_file(cls, file_path):
         """
         Reads initial reaction rates from a file.
 
@@ -206,30 +170,33 @@ def read_initial_rates_from_file(cls, file_path, reaction_list):
 
         Args:
             file_path (str): The path to the file containing the initial reaction rates.
-            reaction_list (ReactionList): A ReactionList containing the reactions involved in the simulation.
 
         Returns:
-            list: A list where each element represents the initial rate of a reaction.
+            dict: A dictionary of initial reaction rates.
         """
 
-        reaction_rates = []
-
-        with open(file_path, 'r') as csv_file:
-            initial_conditions = list(csv.reader(csv_file))
-
-            if (len(initial_conditions) > 1):
-                # The first row of the CSV contains headers
-                headers = initial_conditions[0]
-
-                # The second row of the CSV contains rates
-                rates = initial_conditions[1]
-
-                for reaction_rate, rate in zip(headers, rates):
-                    type, name, *rest = reaction_rate.split('.')
-                    for reaction in reaction_list.reactions:
-                        if reaction.name == name and reaction.short_type() == type:
-                            reaction_rates.append(ReactionRate(reaction, rate))
-
+        reaction_rates = {}
+
+        df = pd.read_csv(file_path)
+        rows, _ = df.shape
+        if rows > 1:
+            raise ValueError(f'Initial conditions file ({file_path}) may only have one row of data. There are {rows} rows present.')
+        for key in df.columns:
+            parts = key.split('.')
+            reaction_type, label = None, None
+            if len(parts) == 3:
+                reaction_type, label, units = parts
+            elif len(parts) == 2:
+                reaction_type, label = parts
+            else:
+                error = f"Unexpected format in key: {key}"
+                logger.error(error)
+                raise ValueError(error)
+            rate_name = f'{reaction_type}.{label}'
+            if rate_name in reaction_rates:
+                raise ValueError(f"Duplicate reaction rate found: {rate_name}")
+            reaction_rates[rate_name] = df.iloc[0][key]
+
         return reaction_rates
 
     def add_species_concentration(self, species_concentration):
@@ -295,18 +262,6 @@ def update_conditions(self, new_conditions):
             self.pressure = new_conditions.pressure
         if new_conditions.temperature is not None:
             self.temperature = new_conditions.temperature
-        for conc in new_conditions.species_concentrations:
-            match = filter(
-                lambda x: x.species.name == conc.species.name,
-                self.species_concentrations)
-            for item in list(match):
-                item.concentration = conc.concentration
-
-        for rate in new_conditions.reaction_rates:
-
-            match = filter(
-                lambda x: x.reaction.name == rate.reaction.name,
-                self.reaction_rates)
+        self.species_concentrations.update(new_conditions.species_concentrations)
 
-            for item in list(match):
-                item.rate = rate.rate
+        self.reaction_rates.update(new_conditions.reaction_rates)

src/acom_music_box/constants.py

@@ -0,0 +1,3 @@
+BOLTZMANN_CONSTANT = 1.380649e-23       # joules / Kelvin
+AVOGADRO_CONSTANT = 6.02214076e23       # / mole
+GAS_CONSTANT = BOLTZMANN_CONSTANT * AVOGADRO_CONSTANT   # joules / Kelvin-mole