function that generates thermo file

photochem/equilibrate.py

@@ -1,2 +1,36 @@
 from ._equilibrate import ChemEquiAnalysis, EquilibrateException
-from ._equilibrate import __version__
+from ._equilibrate import __version__
+from .utils._format import FormatReactions_main, yaml, Loader, MyDumper
+import os
+
+def generate_zahnle_earth_thermo(outfile='zahnle_earth_thermo.yaml'):
+    """Generates a thermodynamic file for equilibrium solving that includes
+    condensible species (e.g., H2O condensate).
+
+    Parameters
+    ----------
+    outfile : str, optional
+        Name of the output file, by default 'zahnle_earth_thermo.yaml'
+    """    
+
+    rx_folder = os.path.dirname(os.path.realpath(__file__))+'/data/reaction_mechanisms/'
+
+    with open(rx_folder+'zahnle_earth.yaml','r') as f:
+        dat = yaml.load(f, Loader=Loader)
+
+    with open(rx_folder+'condensate_thermo.yaml','r') as f:
+        dat1 = yaml.load(f, Loader=Loader)
+
+    # Delete information that is not needed
+    for i,atom in enumerate(dat['atoms']):
+        del dat['atoms'][i]['redox'] 
+    del dat['particles']
+    del dat['reactions']
+
+    for i,sp in enumerate(dat1['species']):
+        dat['species'].append(sp)
+
+    dat = FormatReactions_main(dat)
+
+    with open(outfile, 'w') as f:
+        yaml.dump(dat,f,Dumper=MyDumper,sort_keys=False,width=70)