add allow_max_rate_violation attribute to exempt reactions from the m…

…ax rate requirements
ReactionMechanismGenerator · Jun 11, 2018 · ab2430a · ab2430a
1 parent 09aa3cb
commit ab2430a
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/rmgpy/reaction.pxd b/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)
 

diff --git a/rmgpy/reaction.py b/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):
         """

diff --git a/testing/databaseTest.py b/testing/databaseTest.py
@@ -443,14 +443,14 @@ def kinetics_checkLibraryRatesAreReasonable(self, library):
             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 len(rxn.reactants) == 1 and rxn.allow_max_rate_violation==False:
                 if k > (kB*T)/h:
                     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:
+                    logging.error('library reaction {0} from library {1}, exceeds the TST limit at 1000 K, 1 bar and did not have allow_max_rate_violation=True'.format(rxn,library.label))
+            elif len(rxn.reactants) == 2 and rxn.allow_max_rate_violation==False:
                 if k > Na*np.pi*Hrad_diam**2*np.sqrt(8*kB*T/(np.pi*mHrad/2)):
                     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 and did not have allow_max_rate_violation=True'.format(rxn,library.label)) 
         if boo:
             raise ValueError('library {0} has unreasonable rates'.format(library.label))