exclude species feature

photochem/equilibrate.py

@@ -3,16 +3,18 @@
 from .utils._format import FormatReactions_main, yaml, Loader, MyDumper, mechanism_dict_with_atoms
 from photochem_clima_data import DATA_DIR
 
-def generate_zahnle_earth_thermo(outfile='zahnle_earth_thermo.yaml', atoms_names=None):
+def generate_zahnle_earth_thermo(outfile='zahnle_earth_thermo.yaml', atoms_names=None, exclude_species=[]):
     """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'
-    atoms_names: list, optional
+    atoms_names : list, optional
         List of atoms to keep. By default all atoms in the mechanism are kept
+    exclude_species : list, optional
+        List of species to exclude.
     """    
 
     rx_folder = DATA_DIR+'/reaction_mechanisms/'
@@ -32,8 +34,10 @@ def generate_zahnle_earth_thermo(outfile='zahnle_earth_thermo.yaml', atoms_names
     for i,sp in enumerate(dat1['species']):
         dat['species'].append(sp)
 
-    if atoms_names is not None:
-        dat = mechanism_dict_with_atoms(dat, atoms_names)
+    if atoms_names is None:
+        atoms_names = [a['name'] for a in dat['atoms']]
+
+    dat = mechanism_dict_with_atoms(dat, atoms_names, exclude_species)
 
     dat = FormatReactions_main(dat)
 

photochem/extensions/gasgiants.py

@@ -955,6 +955,7 @@ def generate_photochem_rx_and_thermo_files(
         atoms_names=['H','He','N','O','C','S'], 
         rxns_filename='photochem_rxns.yaml', 
         thermo_filename='photochem_thermo.yaml',
+        exclude_species=[],
         remove_particles=False, 
         remove_reaction_particles=True
     ):
@@ -968,6 +969,8 @@ def generate_photochem_rx_and_thermo_files(
         Name of output reactions file, by default 'photochem_rxns.yaml'
     thermo_filename : str, optional
         Name of output thermodynamic file, by default 'photochem_thermo.yaml'
+    exclude_species : list, optional
+        List of species to exclude.
     remove_particles : bool, optional
         If True, then particles will be removed, by default False.
     remove_reaction_particles : bool, optional
@@ -976,11 +979,11 @@ def generate_photochem_rx_and_thermo_files(
     # Kinetics
     with open(zahnle_earth,'r') as f:
         rxns = yaml.load(f,Loader=yaml.Loader)
-    rxns = mechanism_dict_with_atoms(rxns, atoms_names, remove_particles, remove_reaction_particles)
+    rxns = mechanism_dict_with_atoms(rxns, atoms_names, exclude_species, remove_particles, remove_reaction_particles)
     rxns = FormatReactions_main(rxns)
     with open(rxns_filename,'w') as f:
         yaml.dump(rxns,f,Dumper=MyDumper,sort_keys=False,width=70)
 
     # Thermodynamics
-    equilibrate.generate_zahnle_earth_thermo(thermo_filename, atoms_names)
+    equilibrate.generate_zahnle_earth_thermo(thermo_filename, atoms_names, exclude_species)
 

photochem/utils/_format.py

@@ -177,7 +177,12 @@ def FormatSettings_main(data):
 
     return data
 
-def mechanism_dict_with_atoms(dat, atoms_names, remove_particles=False, remove_reaction_particles=False):
+def species_in_reaction(rx):
+    rx1 = rx.replace('<=>','=>').replace('(','').replace(')','')
+    react, prod = [a.replace(' ','').split('+') for a in rx1.split('=>')]
+    return react + prod
+
+def mechanism_dict_with_atoms(dat, atoms_names, exclude_species=[], remove_particles=False, remove_reaction_particles=False):
 
     atoms = []
     exclude_atoms = []
@@ -199,6 +204,10 @@ def mechanism_dict_with_atoms(dat, atoms_names, remove_particles=False, remove_r
             if tmp in exclude_atoms:
                 exclude = True
                 break
+
+        if sp['name'] in exclude_species:
+            exclude = True
+
         if not exclude:
             species.append(sp)
 
@@ -215,26 +224,24 @@ def mechanism_dict_with_atoms(dat, atoms_names, remove_particles=False, remove_r
 
             if remove_reaction_particles and sp['formation'] == "reaction":
                 exclude = True
+
+            if sp['name'] in exclude_species:
+                exclude = True
+            if sp['formation'] == "saturation":
+                if sp['gas-phase'] in exclude_species:
+                    exclude = True
+            elif not remove_reaction_particles and sp['formation'] == "reaction":
+                rx_sp = species_in_reaction(sp['equation'])
+                if any(a in exclude_species for a in rx_sp):
+                    exclude = True
 
             if not exclude:
                 particles.append(sp)
 
     if "reactions" in dat:
         reactions = []
         for i,rx in enumerate(dat['reactions']):
-            eq = rx['equation']
-            eq = eq.replace('(','').replace(')','')
-            if '<=>' in eq:
-                split_str = '<=>'
-            else:
-                split_str = '=>'
-
-            a,b = eq.split(split_str)
-            a = a.split('+')
-            b = b.split('+')
-            a = [a1.strip() for a1 in a]
-            b = [b1.strip() for b1 in b]
-            sp = a + b
+            sp = species_in_reaction(rx['equation'])
 
             exclude = False
             for s in sp:
@@ -244,6 +251,10 @@ def mechanism_dict_with_atoms(dat, atoms_names, remove_particles=False, remove_r
                         break
                 if exclude:
                     break
+
+            if any(a in exclude_species for a in sp):
+                exclude = True
+
             if not exclude:
                 reactions.append(rx)
 
@@ -257,14 +268,15 @@ def mechanism_dict_with_atoms(dat, atoms_names, remove_particles=False, remove_r
 
     return out
 
-def resave_mechanism_with_atoms(infile, outfile, atoms_names, remove_particles=False, remove_reaction_particles=False):
+def resave_mechanism_with_atoms(infile, outfile, atoms_names, exclude_species=[], remove_particles=False, remove_reaction_particles=False):
 
     with open(infile,'r') as f:
         dat = yaml.load(f,Loader=Loader)
 
     out = mechanism_dict_with_atoms(
         dat, 
         atoms_names, 
+        exclude_species,
         remove_particles,
         remove_reaction_particles
     )

setup.py

@@ -14,7 +14,7 @@
 
 setup(
     name="photochem",
-    packages=['photochem','photochem.utils'],
+    packages=['photochem','photochem.utils','photochem.extensions'],
     python_requires='>=3.6',
     version=version,
     license="GNU General Public License v3.0",