EVERYTHING ELSE from cat branch

ReactionMechanismGenerator · Jan 25, 2019 · 030761c · 030761c
1 parent dac978b
commit 030761c
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Showing 4 changed files with 7 additions and 3 deletions.
diff --git a/rmgpy/molecule/adjlist.py b/rmgpy/molecule/adjlist.py
@@ -35,6 +35,7 @@
 import logging
 import warnings
 import re
+import numpy as np
 from .molecule import Atom, Bond, getAtomType
 from .group import GroupAtom, GroupBond
 from .element import getElement, PeriodicSystem

diff --git a/rmgpy/molecule/group.py b/rmgpy/molecule/group.py
@@ -2329,7 +2329,7 @@ def pickWildcards(self):
                     atom2.bonds[atom1].order = bond12.order
                     continue
 
-                atom1Bonds = atom1.countBonds()
+                atom1Bonds = atom1.countBonds() # countBonds list must match getFeatures list
                 atom2Bonds = atom2.countBonds()
                 requiredFeatures1 = [atom1Features[x][0] - atom1Bonds[x] if atom1Features[x] else 0 for x in range(len(atom1Bonds))]
                 requiredFeatures2 = [atom2Features[x][0] - atom2Bonds[x] if atom2Features[x] else 0 for x in range(len(atom2Bonds))]

diff --git a/rmgpy/rmg/main.py b/rmgpy/rmg/main.py
@@ -364,6 +364,9 @@ def loadDatabase(self):
         #check libraries
         self.checkLibraries()
 
+        if self.bindingEnergies:
+            self.database.thermo.setDeltaAtomicAdsorptionEnergies(self.bindingEnergies)
+
         #set global variable solvent
         if self.solvent:
             global solvent
@@ -937,12 +940,11 @@ def execute(self, **kwargs):
                 self.generateCanteraFiles(os.path.join(self.outputDirectory, 'chemkin', 'chem.inp'))
                 self.generateCanteraFiles(os.path.join(self.outputDirectory, 'chemkin', 'chem_annotated.inp'))
         except EnvironmentError:
-            logging.error('Could not generate Cantera files due to EnvironmentError. Check read\write privileges in output directory.')
+            logging.exception('Could not generate Cantera files due to EnvironmentError. Check read\write privileges in output directory.')
         except Exception:
             logging.exception('Could not generate Cantera files for some reason.')
 
         self.check_model()
-
         # Write output file
         logging.info('')
         logging.info('MODEL GENERATION COMPLETED')

diff --git a/rmgpy/solver/base.pyx b/rmgpy/solver/base.pyx
@@ -207,6 +207,7 @@ cdef class ReactionSystem(DASx):
 
         if conditions:
             isConc = hasattr(self,'initialConcentrations')
+            # ToDo: I think this block is incompatible with surface.pyx catalyst reactors
             keys = conditions.keys()
             if 'T' in keys and hasattr(self,'T'):
                 self.T = Quantity(conditions['T'],'K')