Merge branch 'main' into release

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: v2.5.0
+version: v2.5.5
 authors:
   - family-names: Dawson
     given-names: Matthew

pyproject.toml

@@ -26,7 +26,9 @@ dependencies = [
   "colorlog",
   "pandas",
   "tqdm",
-  "netcdf4"
+  "netcdf4",
+  "matplotlib",
+  "mplcursors"
 ]
 
 [project.urls]

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__ = "2.5.4"
+__version__ = "2.5.5"
 
 from .utils import convert_time, convert_pressure, convert_temperature, convert_concentration
 from .model_options import BoxModelOptions

src/acom_music_box/examples/configs/ts1/my_config.json

@@ -411,6 +411,15 @@
     },
     "TEPOMUC": {
       "initial value [mol m-3]": 1.86716E-11
+    },
+    "O2": {
+      "initial value [mol m-3]": 8.368900382
+    },
+    "N2": {
+      "initial value [mol m-3]": 31.08448713
+    },
+    "H2O": {
+      "initial value [mol m-3]": 1.195557197
     }
   },
   "environmental conditions": {

src/acom_music_box/main.py

@@ -6,6 +6,8 @@
 import subprocess
 import sys
 import tempfile
+import matplotlib.pyplot as plt
+import mplcursors
 from acom_music_box import MusicBox, Examples, __version__
 
 
@@ -55,6 +57,13 @@ def parse_arguments():
         type=str,
         help='Plot a comma-separated list of species if gnuplot is available (e.g., CONC.A,CONC.B).'
     )
+    parser.add_argument(
+        '--plot-tool',
+        type=str,
+        choices=['gnuplot', 'matplotlib'],
+        default='matplotlib',
+        help='Choose plotting tool: gnuplot or matplotlib (default: matplotlib).'
+    )
     return parser.parse_args()
 
 
@@ -119,6 +128,33 @@ def plot_with_gnuplot(data, species_list):
             os.remove(data_file_path)
 
 
+def plot_with_matplotlib(data, species_list):
+    # Prepare columns and data for plotting
+    indexed = data.set_index('time')
+
+    fig, ax = plt.subplots()
+    indexed[species_list].plot(ax=ax)
+
+    ax.set(xlabel='Time [s]', ylabel='Concentration [mol m-3]', title='Time vs Species')
+
+    ax.spines[:].set_visible(False)
+    ax.spines['left'].set_visible(True)
+    ax.spines['bottom'].set_visible(True)
+
+    ax.grid(alpha=0.5)
+    ax.legend()
+
+    # Enable interactive data cursors with hover functionality
+    cursor = mplcursors.cursor(hover=True)
+
+    # Customize the annotation format
+    @cursor.connect("add")
+    def on_add(sel):
+        sel.annotation.set_text(f'Time: {sel.target[0]:.2f}\nConcentration: {sel.target[1]:1.2e}')
+
+    plt.show()
+
+
 def main():
     start = datetime.datetime.now()
 
@@ -159,8 +195,10 @@ def main():
         print(result.to_csv(index=False))
 
     if plot_species_list:
-        # Prepare data for plotting
-        plot_with_gnuplot(result, plot_species_list)
+        if args.plot_tool == 'gnuplot':
+            plot_with_gnuplot(result, plot_species_list)
+        elif args.plot_tool == 'matplotlib':
+            plot_with_matplotlib(result, plot_species_list)
 
     end = datetime.datetime.now()
     logger.info(f"End time: {end}")

src/acom_music_box/tools/waccmToMusicBox.py

@@ -220,6 +220,17 @@ def readWACCM(waccmMusicaDict, latitude, longitude,
     return (musicaDict)
 
 
+# Add molecular Nitrogen, Oxygen, and Argon to dictionary.
+# varValues = already read from WACCM, contains (name, concentration, units)
+# return varValues with N2, O2, and Ar added
+def addStandardGases(varValues):
+    varValues["N2"] = ("N2", 0.78084, "mol/mol")    # standard fraction by volume
+    varValues["O2"] = ("O2", 0.20946, "mol/mol")
+    varValues["Ar"] = ("Ar", 0.00934, "mol/mol")
+
+    return (varValues)
+
+
 # set up indexes for the tuple
 musicaIndex = 0
 valueIndex = 1
@@ -268,7 +279,7 @@ def writeInitCSV(initValues, filename):
         else:
             fp.write(",")
 
-        fp.write(key)
+        fp.write("{} [{}]".format(key, value[unitIndex]))
     fp.write("\n")
 
     # write the variable values
@@ -404,9 +415,19 @@ def main():
     if ("longitude" in myArgs):
         lon = safeFloat(myArgs.get("longitude"))
 
+    # get the requested (diagnostic) output
+    outputCSV = False
+    outputJSON = False
+    if ("output" in myArgs):
+        # parameter is like: output=CSV,JSON
+        outputFormats = myArgs.get("output").split(",")
+        outputFormats = [lowFormat.lower() for lowFormat in outputFormats]
+        outputCSV = "csv" in outputFormats
+        outputJSON = "json" in outputFormats
+
+    # locate the WACCM output file
     when = datetime.datetime.strptime(
         f"{dateStr} {timeStr}", "%Y%m%d %H:%M")
-
     waccmFilename = f"f.e22.beta02.FWSD.f09_f09_mg17.cesm2_2_beta02.forecast.001.cam.h3.{when.year:4d}-{when.month:02d}-{when.day:02}-00000.nc"
 
     # read and glean chemical species from WACCM and MUSICA
@@ -425,16 +446,19 @@ def main():
                           lat, lon, when, waccmDir, waccmFilename)
     logger.info(f"Original WACCM varValues = {varValues}")
 
+    # add molecular Nitrogen, Oxygen, and Argon
+    varValues = addStandardGases(varValues)
+
     # Perform any conversions needed, or derive variables.
     varValues = convertWaccm(varValues)
     logger.info(f"Converted WACCM varValues = {varValues}")
 
-    if (False):
+    if (outputCSV):
         # Write CSV file for MusicBox initial conditions.
         csvName = os.path.join(musicaDir, "initial_conditions.csv")
         writeInitCSV(varValues, csvName)
 
-    if (False):
+    if (outputJSON):
         # Write JSON file for MusicBox initial conditions.
         jsonName = os.path.join(musicaDir, "initial_config.json")
         writeInitJSON(varValues, jsonName)