add allow_max_rate_violation attribute to exempt reactions from the m…

…ax rate requirements

rmgpy/data/kinetics/common.py

@@ -87,6 +87,8 @@ def sortEfficiencies(efficiencies0):
                 f.write('    allow_pdep_route = {0!r},\n'.format(entry.item.allow_pdep_route))
             if entry.item.elementary_high_p:
                 f.write('    elementary_high_p = {0!r},\n'.format(entry.item.elementary_high_p))
+            if entry.item.allow_max_rate_violation:
+                f.write('    allow_max_rate_violation = {0!r},\n'.format(entry.item.allow_max_rate_violation))
     #Entries for groups with have a group or logicNode for its item
     elif isinstance(entry.item, Group):
         f.write('    group = \n')

rmgpy/data/kinetics/library.py

@@ -77,7 +77,8 @@ def __init__(self,
                  library=None,
                  allow_pdep_route=False,
                  elementary_high_p=False,
-                 entry=None
+                 allow_max_rate_violation=False,
+                 entry=None,
                  ):
         Reaction.__init__(self,
                           index=index,
@@ -93,6 +94,7 @@ def __init__(self,
                           pairs=pairs,
                           allow_pdep_route=allow_pdep_route,
                           elementary_high_p=elementary_high_p,
+                          allow_max_rate_violation=allow_max_rate_violation,
                           )
         self.library = library
         self.family = library
@@ -116,6 +118,7 @@ def __reduce__(self):
                                   self.library,
                                   self.allow_pdep_route,
                                   self.elementary_high_p,
+                                  self.allow_max_rate_violation,
                                   self.entry
                                   ))
 
@@ -463,6 +466,7 @@ def loadEntry(self,
                   longDesc='',
                   allow_pdep_route=False,
                   elementary_high_p=False,
+                  allow_max_rate_violation=False,
                   ):
 
 #        reactants = [Species(label=reactant1.strip().splitlines()[0].strip(), molecule=[Molecule().fromAdjacencyList(reactant1)])]
@@ -475,7 +479,7 @@ def loadEntry(self,
 #        
         # Make a blank reaction
         rxn = Reaction(reactants=[], products=[], degeneracy=degeneracy, duplicate=duplicate, reversible=reversible,
-                       allow_pdep_route=allow_pdep_route, elementary_high_p=elementary_high_p)
+                       allow_pdep_route=allow_pdep_route, elementary_high_p=elementary_high_p, allow_max_rate_violation=allow_max_rate_violation)
 #        if not rxn.isBalanced():
 #            raise DatabaseError('Reaction {0} in kinetics library {1} was not balanced! Please reformulate.'.format(rxn, self.label))        
 #        label = str(rxn)

rmgpy/reaction.pxd

@@ -54,6 +54,7 @@ cdef class Reaction:
     cdef public bint elementary_high_p
     cdef public str comment
     cdef public dict k_effective_cache
+    cdef public bint allow_max_rate_violation
 
     cpdef bint isIsomerization(self)
 

rmgpy/reaction.py

@@ -104,6 +104,7 @@ def __init__(self,
                  pairs=None,
                  allow_pdep_route=False,
                  elementary_high_p=False,
+                 allow_max_rate_violation=False,
                  comment='',
                  ):
         self.index = index
@@ -122,6 +123,7 @@ def __init__(self,
         self.elementary_high_p = elementary_high_p
         self.comment = comment
         self.k_effective_cache = {}
+        self.allow_max_rate_violation = allow_max_rate_violation
 
     def __repr__(self):
         """

testing/databaseTest.py

@@ -437,20 +437,22 @@ def kinetics_checkLibraryRatesAreReasonable(self, library):
         kB = 1.38064852e-23 #m2 * kg *s^-2 * K^-1
         h = 6.62607004e-34 #m2 kg / s
         boo = False
+        TST_limit = (kB*T)/h
+        collision_limit = Na*np.pi*Hrad_diam**2*np.sqrt(8*kB*T/(np.pi*mHrad/2))
         for entry in library.entries.values():
             k = entry.data.getRateCoefficient(T,P)
             rxn = entry.item
             if k < 0:
                 boo = True
                 logging.error('library reaction {0} from library {1}, had a negative rate at 1000 K, 1 bar'.format(rxn,library.label))
-            if len(rxn.reactants) == 1:
-                if k > (kB*T)/h:
+            if len(rxn.reactants) == 1 and rxn.allow_max_rate_violation==False:
+                if k > TST_limit:
                     boo = True
-                    logging.error('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar'.format(rxn,library.label))
-            elif len(rxn.reactants) == 2:
-                if k > Na*np.pi*Hrad_diam**2*np.sqrt(8*kB*T/(np.pi*mHrad/2)):
+                    logging.error('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar of {2} mol/(m3*s) at {3} mol/(m3*s) and did not have allow_max_rate_violation=True'.format(rxn,library.label,TST_limit,k))
+            elif len(rxn.reactants) == 2 and rxn.allow_max_rate_violation==False:
+                if k > collision_limit:
                     boo = True
-                    logging.error('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar'.format(rxn,library.label)) 
+                    logging.error('library reaction {0} from library {1}, exceeds the collision limit at 1000 K, 1 bar of {2} mol/(m3*s) at {3} mol/(m3*s) and did not have allow_max_rate_violation=True'.format(rxn,library.label,collision_limit,k)) 
         if boo:
             raise ValueError('library {0} has unreasonable rates'.format(library.label))