Allows constant concentration species in simple gas phase reactors

rmgpy/rmg/input.py

@@ -190,7 +190,7 @@ def simple_reactor(temperature,
                    sensitivityTemperature=None,
                    sensitivityPressure=None,
                    sensitivityMoleFractions=None,
-                   ):
+                   constantSpecies=None):
     logging.debug('Found SimpleReactor reaction system')
 
     for key, value in initialMoleFractions.items():
@@ -249,7 +249,15 @@ def simple_reactor(temperature,
         else:
             sensitive_species.append('all')
 
-    if not isinstance(T, list):
+    #Check the constant species exist
+    if constantSpecies is not None:
+        logging.debug('  Generation with constant species:')
+        for constantSpecie in constantSpecies:
+            logging.debug("  {0}".format(constantSpecie))
+            if constantSpecie not in species_dict:
+                raise InputError('Species {0} not found in the input file'.format(constantSpecie))
+
+    if not isinstance(T,list):
         sensitivityTemperature = T
     if not isinstance(P, list):
         sensitivityPressure = P
@@ -262,8 +270,7 @@ def simple_reactor(temperature,
         sens_conditions['T'] = Quantity(sensitivityTemperature).value_si
         sens_conditions['P'] = Quantity(sensitivityPressure).value_si
 
-    system = SimpleReactor(T, P, initialMoleFractions, nSims, termination, sensitive_species, sensitivityThreshold,
-                           sens_conditions)
+    system = SimpleReactor(T, P, initialMoleFractions, nSims, termination, sensitive_species, sensitivityThreshold, sens_conditions, constantSpecies)
     rmg.reaction_systems.append(system)
 
     assert balanceSpecies is None or isinstance(balanceSpecies, str), 'balanceSpecies should be the string corresponding to a single species'

rmgpy/solver/mbSampled.pyx

@@ -64,6 +64,7 @@ cdef class MBSampledReactor(ReactionSystem):
     cdef public bint constant_volume
     cdef public dict initial_mole_fractions
     cdef public list constantSpeciesList
+    cdef public list const_spc_names 
 
     # collider variables
 
@@ -112,13 +113,14 @@ cdef class MBSampledReactor(ReactionSystem):
     cdef public np.ndarray pdep_specific_collider_reaction_indices
 
     def __init__(self, T, P, initial_mole_fractions, k_sampling, constantSpeciesList, termination, sensitive_species=None,
-                 sensitivity_threshold=1e-3):
+                 sensitivity_threshold=1e-3, const_spc_names=None):
         ReactionSystem.__init__(self, termination, sensitive_species, sensitivity_threshold)
         self.T = Quantity(T)
         self.P = Quantity(P)
         self.initial_mole_fractions = initial_mole_fractions
         self.k_sampling = RateCoefficient(k_sampling)
         self.constantSpeciesList = constantSpeciesList
+        self.const_spc_names = const_spc_names
 
         self.V = 0  # will be set in initialize_model
         self.constant_volume = False

rmgpy/solver/simple.pyx

@@ -56,6 +56,8 @@ cdef class SimpleReactor(ReactionSystem):
     cdef public double V
     cdef public bint constant_volume
     cdef public dict initial_mole_fractions
+    cdef public list const_spc_names 
+    cdef public list const_spc_indices
 
     # collider variables
 
@@ -110,7 +112,7 @@ cdef class SimpleReactor(ReactionSystem):
     cdef public int n_sims
 
     def __init__(self, T, P, initial_mole_fractions, n_sims=1, termination=None, sensitive_species=None,
-                 sensitivity_threshold=1e-3, sens_conditions=None):
+                 sensitivity_threshold=1e-3, sens_conditions=None, const_spc_names=None):
         ReactionSystem.__init__(self, termination, sensitive_species, sensitivity_threshold)
 
         if type(T) != list:
@@ -125,6 +127,10 @@ cdef class SimpleReactor(ReactionSystem):
 
         self.initial_mole_fractions = initial_mole_fractions
 
+        #Constant Species Properties
+        self.const_spc_indices=None
+        self.const_spc_names = const_spc_names #store index of constant species 
+
         self.V = 0  # will be set in initialize_model
         self.constant_volume = False
 
@@ -163,6 +169,15 @@ cdef class SimpleReactor(ReactionSystem):
                     conditions[species_dict[label]] = value
         self.sens_conditions = conditions
 
+    def get_const_spc_indices (self, coreSpecies):
+        "Allow to identify constant Species position in solver"
+        for spc in self.const_spc_names:
+            if self.const_spc_indices is None: #initialize once the list if constant SPC declared
+                self.const_spc_indices=[]
+            for iter in coreSpecies: #Need to identify the species object corresponding to the the string written in the input file
+                if iter.label == spc:
+                    self.const_spc_indices.append(coreSpecies.index(iter))#get 
+
     cpdef initialize_model(self, list core_species, list core_reactions, list edge_species, list edge_reactions,
                           list surface_species=None, list surface_reactions=None, list pdep_networks=None,
                           atol=1e-16, rtol=1e-8, sensitivity=False, sens_atol=1e-6, sens_rtol=1e-4,
@@ -504,6 +519,10 @@ cdef class SimpleReactor(ReactionSystem):
                 reaction_rate = k * C[inet[j, 0]] * C[inet[j, 1]] * C[inet[j, 2]]
             network_leak_rates[j] = reaction_rate
 
+        if self.const_spc_indices is not None:
+            for spcIndice in self.const_spc_indices:
+                core_species_rates[spcIndice] = 0
+
         self.core_species_concentrations = core_species_concentrations
         self.core_species_rates = core_species_rates
         self.core_species_production_rates = core_species_production_rates

rmgpy/tools/simulate.py

@@ -84,14 +84,14 @@ def simulate(rmg, diffusion_limited=True):
                 rmg.load_database()
                 solvent_data = rmg.database.solvation.get_solvent_data(rmg.solvent)
                 diffusion_limiter.enable(solvent_data, rmg.database.solvation)
-
-            # Store constant species indices
-            if reaction_system.const_spc_names is not None:
-                reaction_system.get_const_spc_indices(rmg.reaction_model.core.species)
         elif rmg.uncertainty is not None:
             rmg.verbose_comments = True
             rmg.load_database()
 
+	# Store constant species indices
+        if reaction_system.const_spc_names is not None:
+            reaction_system.get_const_spc_indices(rmg.reaction_model.core.species)
+
         reaction_system.simulate(
             core_species=rmg.reaction_model.core.species,
             core_reactions=rmg.reaction_model.core.reactions,