Progress on implementing temperature scanning calculations -- SO--

core/ElementaryReaction.py

@@ -113,6 +113,10 @@ def __init__(self,
         self.__label = None
         self.__updateLabel()
 
+        # Hidden attributes. Only for using with AMS
+        self._kf_prefactors_forward = RKFPrefactors()
+        self._kf_prefactors_backward = RKFPrefactors()
+
 
     def __eq__(self, other):
         """
@@ -325,3 +329,14 @@ def replace_site_types( self, site_types_old, site_types_new ):
                     self.site_types[j] = site_types_new[i]
 
         self.__updateLabel()
+
+
+    def set_temperature( self, temperature ):
+        """
+        Sets the temperature of the reaction. It recalculates the pre-exponential factors if needed.
+
+        *   ``temperature`` -- Temperature in K
+        """
+
+        for erxn in self:
+            erxn.set_temperature( temperature )

core/Mechanism.py

@@ -345,3 +345,13 @@ def find_one( self, label ):
         """
         return next(rxn for rxn in self if rxn.label().find(label) != -1)
 
+
+    def set_temperature( self, temperature ):
+        """
+        Sets the temperature of the mechanism. It recalculates the pre-exponential factors if needed.
+
+        *   ``temperature`` -- Temperature in K
+        """
+
+        for erxn in self:
+            erxn.set_temperature( temperature )

core/RKFLoader.py

@@ -60,6 +60,7 @@ def __deriveLatticeAndMechanism( self, results ):
         isTS = results.readrkf("EnergyLandscape", "isTS")
         reactants = results.readrkf("EnergyLandscape", "reactants")
         products = results.readrkf("EnergyLandscape", "products")
+        prefactorsTemperature = results.readrkf("EnergyLandscape", "prefactorsTemperature")
         prefactorsFromReactant = results.readrkf("EnergyLandscape", "prefactorsFromReactant")
         prefactorsFromProduct = results.readrkf("EnergyLandscape", "prefactorsFromProduct")
 
@@ -491,6 +492,11 @@ def getGasFormationEnergy( mol, energy ):
                                                pe_ratio=pe_ratio,
                                                activation_energy=activationEnergy )
 
+                reaction._prefactors_temperature = prefactorsTemperature
+                reaction._prefactors_model = REACTION_MEDIATED_BY_A_TRANSITION_STATE
+                reaction._kf_reactants = fileName[idReactant]
+                reaction._kf_products = fileName[idProduct]
+
                 #self.clusterExpansion.extend( [clusterReactant, clusterProduct] )
                 self.mechanism.append( reaction )
 
@@ -543,14 +549,18 @@ def getGasFormationEnergy( mol, energy ):
                 activationEnergy = 0.0 if state2Energy[idState]<energy else state2Energy[idState]-energy
 
                 reaction = ElementaryReaction( site_types=cluster_data['site_types'],
-                                            final_entity_number=cluster_data['entity_number'],
-                                            neighboring=cluster_data['neighboring'],
-                                            initial=speciesFState,
-                                            final=cluster_data['species'],
-                                            reversible=True,
-                                            pre_expon=prefactorAdsorption,
-                                            pe_ratio=pe_ratio,
-                                            activation_energy=activationEnergy )
+                                               final_entity_number=cluster_data['entity_number'],
+                                               neighboring=cluster_data['neighboring'],
+                                               initial=speciesFState,
+                                               final=cluster_data['species'],
+                                               reversible=True,
+                                               pre_expon=prefactorAdsorption,
+                                               pe_ratio=pe_ratio,
+                                               activation_energy=activationEnergy)
+
+                reaction._prefactorsTemperature = prefactorsTemperature
+                reaction._kf_reactants = fileName[idReactant]
+                reaction._kf_fragments = fileName[idProduct]
 
                 self.clusterExpansion.extend( [clusterState] )
                 self.mechanism.append( reaction )

core/RKFPrefactors.py

@@ -0,0 +1,70 @@
+import chemparse
+
+__all__ = ['RKFPrefactors']
+
+class RKFPrefactors:
+    """
+    Contains the information needed to calculate the prefactors based on kf files from an AMS calculation
+
+    *   ``temperature`` --
+    *   ``kf_initial`` --
+    *   ``kf_final`` --
+
+    Example
+
+    kind = MEDIATED_BY_A_TRANSITION_STATE
+    kf_initial = 'State-1_MIN.rkf'
+    kf_final = 'State-4_TS_1-3.rkf'
+
+    kind = NON_ACTIVATED_EXOTHERMIC_DESORPTION
+    kf_initial = 'State-1_MIN.rkf'
+    kf_final = ['Fragment-1.rkf', 'Fragment-2.rkf']
+
+    kind = NON_ACTIVATED_EXOTHERMIC_ADSORPTION
+    kf_initial = ['Fragment-1.rkf', 'Fragment-2.rkf']
+    kf_final = None
+    """
+
+    UNSPECIFIED = -1
+    MEDIATED_BY_A_TRANSITION_STATE = 0
+    NON_ACTIVATED_EXOTHERMIC_ADSORPTION = 1
+    NON_ACTIVATED_EXOTHERMIC_DESORPTION = 2
+
+    def __init__(self, temperature=None, kind=None, kf_initial=None, kf_final=None ):
+        """
+        Creates a new RKFPrefactors object.
+        """
+        self.temperature = temperature
+        self.kind = kind
+        self.kf_initial = kf_initial
+        self.kf_final = kf_final
+
+
+    def __eq__( self, other ):
+        """
+        Returns True if both objects are the same (same temperature, and kf files)
+
+        *   ``other`` --
+        """
+        if( type(other) == int and other == Species.UNSPECIFIED ):
+            return False
+
+        if( self.symbol == other.symbol ):
+            return True
+        else:
+            return False
+
+
+    def __hash__(self):
+        """
+        Returns a hash based on the symbol.
+        """
+        return hash(self.symbol)
+
+
+    def __str__( self ):
+        """
+        Translates the object to a string
+        """
+        output  = self.symbol
+        return output

core/ZacrosJob.py

@@ -101,6 +101,9 @@ def check_molar_fraction(settings=Settings, species_list=SpeciesList):
         self.mechanism = mechanism
         if( type(mechanism) == list ): self.mechanism = Mechanism(mechanism)
 
+        if( 'temperature' in kwargs['settings'] ):
+            self.mechanism.set_temperature( kwargs['settings']['temperature'] )
+
         #if( set(map(type, self.mechanism.site_types_set())) == {int} )
 
         if( not self.mechanism.site_types_set().issubset( self.lattice.site_types_set() ) ):